[gmx-users] Umbrella sampling

[Rose]

Hello

I'm beginner in GROMACS. I'm using umbrella sampling(helping from its tutorial with MR Lemkul) But I don't know how should I implement deltaZ and how choose different conf.gro and which will be useful for further sampling.
To tell the truth I couldn't get summary.dat by "perl distance.pl" command.as I'm not good in programming I couldn't understand what happened there?!
How did you know for example:
50>>>0.6 nm
100>>>0.8 nm

I need deltaz=0.05nm

Please help me, i don't know where should i find these informations and modify them.

2- I want that reaction coordinate across Z axes, from slab to 1.5nm far from it (and rvdw and coulomb=1.5 and rlist=1.2) but it moves from1.5nm to for example 3nm and getting closer to wall(4nm far from slab) except slab.
What is my mistake?!

I really need your help.

Best Regards

Rose

Sent from my iPhone
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[Justin Lemkul]

On 11/24/17 9:14 AM, Rose wrote:
> Hello
>
> I'm beginner in GROMACS. I'm using umbrella sampling(helping from its tutorial with MR Lemkul) But I don't know how should I implement deltaZ and how choose different conf.gro and which will be useful for further sampling.
> To tell the truth I couldn't get summary.dat by "perl distance.pl" command.as I'm not good in programming I couldn't understand what happened there?!

Run gmx distance manually. It's probably returning some error, so the
script fails. I've heard this reported a number of times and no one's
ever told me what the solution is, so unfortunately there's nothing I
can do to fix it.

> How did you know for example:
> 50>>>0.6 nm
> 100>>>0.8 nm

This is what gmx distance computes.

> I need deltaz=0.05nm

Then you will need to save frames very frequently. This is a very narrow
dz, and may be overkill depending on what the system is.

> Please help me, i don't know where should i find these informations and modify them.
>
> 2- I want that reaction coordinate across Z axes, from slab to 1.5nm far from it (and rvdw and coulomb=1.5 and

What force field uses such a cutoff? Don't make ad hoc changes to the
cutoffs used by any given force field, as you will get unexpected (or
invalid) results...

> rlist=1.2) but it moves from1.5nm to for example 3nm and getting closer to wall(4nm far from slab) except slab.
> What is my mistake?!

You'll have to provide an .mdp file and a complete description of your
system, how you constructed it, and what your objectives are. Images
would help.

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

***@vt.edu | [phone]
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================

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[rose rahmani]

I attached md_pull.mdp file

i put " cutoff-scheme = group" beecause of some errors (about energy groups)

This is what i try to do(part of some literatures);
1-pulling the CM of the object along the z-axis—perpendicular to the
surface of ZnO

2-Pulling is implemented through a “dummy particle” which moves towards
the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
and drags the CM by the harmonic force corresponding to the spring
constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
the PMF is averaged laterally

3-The conformations are scanned every 0.1 ps in order to save them
with the CM within each of the interval of width 0.05 nm. ( most of
all i'm not sure about this part of my mdp file and i don't know how
should i implement them).

4-between 36-38 conformations should be collected and i dont know how
should i choose them between 710 conf.gro files( i got 710
conformations after using trajconv)

this is first part of my job.

protein is between ZnO and wall and 1.5 nm far from ZnO at first moment.

what do you think about mdp file? where did i make a mistake?

Thank you for your attentions (like always ;) )

Best Regards





Sent from my iPhone

> On Nov 24, 2017, at 19:34, Justin Lemkul <***@vt.edu> wrote:
>
>
>
>> On 11/24/17 9:14 AM, Rose wrote:
>> Hello
>>
>> I'm beginner in GROMACS. I'm using umbrella sampling(helping from its tutorial with MR Lemkul) But I don't know how should I implement deltaZ and how choose different conf.gro and which will be useful for further sampling.
>> To tell the truth I couldn't get summary.dat by "perl distance.pl" command.as I'm not good in programming I couldn't understand what happened there?!
>
> Run gmx distance manually. It's probably returning some error, so the script fails. I've heard this reported a number of times and no one's ever told me what the solution is, so unfortunately there's nothing I can do to fix it.
>
>> How did you know for example:
>> 50>>>0.6 nm
>> 100>>>0.8 nm
>
> This is what gmx distance computes.
>
>> I need deltaz=0.05nm
>
> Then you will need to save frames very frequently. This is a very narrow dz, and may be overkill depending on what the system is.
>
>> Please help me, i don't know where should i find these informations and modify them.
>>
>> 2- I want that reaction coordinate across Z axes, from slab to 1.5nm far from it (and rvdw and coulomb=1.5 and
>
> What force field uses such a cutoff? Don't make ad hoc changes to the cutoffs used by any given force field, as you will get unexpected (or invalid) results...
>
>> rlist=1.2) but it moves from1.5nm to for example 3nm and getting closer to wall(4nm far from slab) except slab.
>> What is my mistake?!
>
> You'll have to provide an .mdp file and a complete description of your system, how you constructed it, and what your objectives are. Images would help.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> ***@vt.edu | [phone]
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-***@gromacs.org.

[Justin Lemkul]

On 11/24/17 3:32 PM, rose rahmani wrote:
> I attached md_pull.mdp file
>
> i put " cutoff-scheme = group" beecause of some errors (about energy groups)

The use of energygrps has no effect on the physics. You should view
pairwise interactions energies as an analysis method, not something that
you need to do as part of your MD run. Don't base your algorithm choices
on a quantity that is usually meaningless.

> This is what i try to do(part of some literatures);
> 1-pulling the CM of the object along the z-axis—perpendicular to the
> surface of ZnO
>
> 2-Pulling is implemented through a “dummy particle” which moves towards
> the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
> and drags the CM by the harmonic force corresponding to the spring
> constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
> the PMF is averaged laterally
>
> 3-The conformations are scanned every 0.1 ps in order to save them
> with the CM within each of the interval of width 0.05 nm. ( most of
> all i'm not sure about this part of my mdp file and i don't know how
> should i implement them).

I don't know what .mdp setting you're referring to here.

> 4-between 36-38 conformations should be collected and i dont know how
> should i choose them between 710 conf.gro files( i got 710
> conformations after using trajconv)

Calculate the COM distance between the groups for each frame. This is
what my tutorial does and what my provided scripts help you to analyze.
Compile a list of the COM distances and determine which frames are
suitable for starting points of each window.

-Justin

> this is first part of my job.
>
> protein is between ZnO and wall and 1.5 nm far from ZnO at first moment.
>
> what do you think about mdp file? where did i make a mistake?
>
> Thank you for your attentions (like always ;) )
>
> Best Regards
>
>
>
>
>
> Sent from my iPhone
>
>> On Nov 24, 2017, at 19:34, Justin Lemkul <***@vt.edu> wrote:
>>
>>
>>
>>> On 11/24/17 9:14 AM, Rose wrote:
>>> Hello
>>>
>>> I'm beginner in GROMACS. I'm using umbrella sampling(helping from its tutorial with MR Lemkul) But I don't know how should I implement deltaZ and how choose different conf.gro and which will be useful for further sampling.
>>> To tell the truth I couldn't get summary.dat by "perl distance.pl" command.as I'm not good in programming I couldn't understand what happened there?!
>> Run gmx distance manually. It's probably returning some error, so the script fails. I've heard this reported a number of times and no one's ever told me what the solution is, so unfortunately there's nothing I can do to fix it.
>>
>>> How did you know for example:
>>> 50>>>0.6 nm
>>> 100>>>0.8 nm
>> This is what gmx distance computes.
>>
>>> I need deltaz=0.05nm
>> Then you will need to save frames very frequently. This is a very narrow dz, and may be overkill depending on what the system is.
>>
>>> Please help me, i don't know where should i find these informations and modify them.
>>>
>>> 2- I want that reaction coordinate across Z axes, from slab to 1.5nm far from it (and rvdw and coulomb=1.5 and
>> What force field uses such a cutoff? Don't make ad hoc changes to the cutoffs used by any given force field, as you will get unexpected (or invalid) results...
>>
>>> rlist=1.2) but it moves from1.5nm to for example 3nm and getting closer to wall(4nm far from slab) except slab.
>>> What is my mistake?!
>> You'll have to provide an .mdp file and a complete description of your system, how you constructed it, and what your objectives are. Images would help.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> ***@vt.edu | [phone]
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-***@gromacs.org.
>>
>>

--
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

***@vt.edu | [phone]
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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[rose rahmani]

On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul <***@vt.edu> wrote:

>
>
> On 11/24/17 3:32 PM, rose rahmani wrote:
>
>> I attached md_pull.mdp file
>>
>> i put " cutoff-scheme = group" beecause of some errors (about energy
>> groups)
>>
>
> The use of energygrps has no effect on the physics. You should view
> pairwise interactions energies as an analysis method, not something that
> you need to do as part of your MD run. Don't base your algorithm choices on
> a quantity that is usually meaningless.
>
> This is what i try to do(part of some literatures);
>> 1-pulling the CM of the object along the z-axis—perpendicular to the
>> surface of ZnO
>>
>> 2-Pulling is implemented through a “dummy particle” which moves towards
>> the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
>> and drags the CM by the harmonic force corresponding to the spring
>> constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
>> the PMF is averaged laterally
>>
>> 3-The conformations are scanned every 0.1 ps in order to save them
>> with the CM within each of the interval of width 0.05 nm. ( most of
>> all i'm not sure about this part of my mdp file and i don't know how
>> should i implement them).
>>
>
> I don't know what .mdp setting you're referring to here.
>
> Sorry, I didn't understand what you mean?

>
> 4-between 36-38 conformations should be collected and i dont know how
>> should i choose them between 710 conf.gro files( i got 710
>> conformations after using trajconv)
>>
>
> Calculate the COM distance between the groups for each frame. This is what
> my tutorial does and what my provided scripts help you to analyze. Compile
> a list of the COM distances and determine which frames are suitable for
> starting points of each window.
>
> -Justin
>
>
> this is first part of my job.
>>
>> protein is between ZnO and wall and 1.5 nm far from ZnO at first moment.
>>
>> what do you think about mdp file? where did i make a mistake?
>>
>> Thank you for your attentions (like always ;) )
>>
>> Best Regards
>>
>>
>>
>>
>>
>> Sent from my iPhone
>>
>> On Nov 24, 2017, at 19:34, Justin Lemkul <***@vt.edu> wrote:
>>>
>>>
>>>
>>> On 11/24/17 9:14 AM, Rose wrote:
>>>> Hello
>>>>
>>>> I'm beginner in GROMACS. I'm using umbrella sampling(helping from its
>>>> tutorial with MR Lemkul) But I don't know how should I implement deltaZ and
>>>> how choose different conf.gro and which will be useful for further sampling.
>>>> To tell the truth I couldn't get summary.dat by "perl distance.pl"
>>>> command.as I'm not good in programming I couldn't understand what
>>>> happened there?!
>>>>
>>> Run gmx distance manually. It's probably returning some error, so the
>>> script fails. I've heard this reported a number of times and no one's ever
>>> told me what the solution is, so unfortunately there's nothing I can do to
>>> fix it.
>>>
>>> How did you know for example:
>>>> 50>>>0.6 nm
>>>> 100>>>0.8 nm
>>>>
>>> This is what gmx distance computes.
>>>
>>> I need deltaz=0.05nm
>>>>
>>> Then you will need to save frames very frequently. This is a very narrow
>>> dz, and may be overkill depending on what the system is.
>>>
>>> Please help me, i don't know where should i find these informations and
>>>> modify them.
>>>>
>>>> 2- I want that reaction coordinate across Z axes, from slab to 1.5nm
>>>> far from it (and rvdw and coulomb=1.5 and
>>>>
>>> What force field uses such a cutoff? Don't make ad hoc changes to the
>>> cutoffs used by any given force field, as you will get unexpected (or
>>> invalid) results...
>>>
>>> rlist=1.2) but it moves from1.5nm to for example 3nm and getting closer
>>>> to wall(4nm far from slab) except slab.
>>>> What is my mistake?!
>>>>
>>> You'll have to provide an .mdp file and a complete description of your
>>> system, how you constructed it, and what your objectives are. Images would
>>> help.
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> ***@vt.edu | [phone]
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-***@gromacs.org.
>>>
>>>
>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> ***@vt.edu | [phone]
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-***@gromacs.org.
>
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[Justin Lemkul]

On 11/25/17 11:49 AM, rose rahmani wrote:
> On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul <***@vt.edu> wrote:
>
>>
>> On 11/24/17 3:32 PM, rose rahmani wrote:
>>
>>> I attached md_pull.mdp file
>>>
>>> i put " cutoff-scheme = group" beecause of some errors (about energy
>>> groups)
>>>
>> The use of energygrps has no effect on the physics. You should view
>> pairwise interactions energies as an analysis method, not something that
>> you need to do as part of your MD run. Don't base your algorithm choices on
>> a quantity that is usually meaningless.
>>
>> This is what i try to do(part of some literatures);
>>> 1-pulling the CM of the object along the z-axis—perpendicular to the
>>> surface of ZnO
>>>
>>> 2-Pulling is implemented through a “dummy particle” which moves towards
>>> the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
>>> and drags the CM by the harmonic force corresponding to the spring
>>> constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
>>> the PMF is averaged laterally
>>>
>>> 3-The conformations are scanned every 0.1 ps in order to save them
>>> with the CM within each of the interval of width 0.05 nm. ( most of
>>> all i'm not sure about this part of my mdp file and i don't know how
>>> should i implement them).
>>>
>> I don't know what .mdp setting you're referring to here.
>>
>> Sorry, I didn't understand what you mean?

The mailing list does not accept attachments, so your .mdp file did not
come through. I'm working blind on what settings you're using. What I
specifically don't understand here is your connection between the
desired spacing along the reaction coordinate and whatever .mdp settings
you think affect this. You can only tell mdrun how frequently to save a
frame, you can't tell it anything about the interval along the reaction
coordinate you care about. Save coordinates frequently enough that you
can plausibly generate a set of configurations to use.

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

***@vt.edu | [phone]
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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[rose rahmani]

Oh sorry this is .mdp file:

DEFINE = -DPOSRES
integrator = md
dt = 0.001
nsteps = 2000000
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 500
nstenergy = 1000
nstxtcout = 1000
rlist = 1.5
rcoulomb = 1.5
rvdw = 1.2
coulombtype = pme
cutoff-scheme = group
vdwtype = Switch
rvdw_switch = 1.0
pcoupl = no
gen-vel = yes
gen-temp = 0
gen-seed = 173529
constraints = h-bonds
pbc = xy
freezegrps = WAL ZnS
freezedim = Y Y Y Y Y Y
energygrp-excl = WAL WAL ZnO ZnO
energygrps = SOL WAL ZnO Protein NA CL
nwall = 2
wall-atomtype = C C
wall-type = 9-3
wall-density = 150 150
wall-ewald-zfac = 3
ewald-geometry = 3dc
fourierspacing = 0.12
tcoupl = v-rescale
tc-grps = System
tau-t = 0.1
ref-t = 300
pull = yes
pull_ngroups = 2
pull_ncoords = 1
pull_group1_name = ZnS
pull_group2_name = Protein-H
pull_coord1_type = umbrella ; harmonic biasing force
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_groups = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate = 0.001
pull_coord1_k = 5000 ; kJ mol^-1 nm^-2
pull_coord1_start = yes ; define initial COM distance > 0


On Sat, Nov 25, 2017 at 11:26 PM, Justin Lemkul <***@vt.edu> wrote:

>
>
> On 11/25/17 11:49 AM, rose rahmani wrote:
>
>> On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul <***@vt.edu> wrote:
>>
>>
>>> On 11/24/17 3:32 PM, rose rahmani wrote:
>>>
>>> I attached md_pull.mdp file
>>>>
>>>> i put " cutoff-scheme = group" beecause of some errors (about energy
>>>> groups)
>>>>
>>>> The use of energygrps has no effect on the physics. You should view
>>> pairwise interactions energies as an analysis method, not something that
>>> you need to do as part of your MD run. Don't base your algorithm choices
>>> on
>>> a quantity that is usually meaningless.
>>>
>>> This is what i try to do(part of some literatures);
>>>
>>>> 1-pulling the CM of the object along the z-axis—perpendicular to the
>>>> surface of ZnO
>>>>
>>>> 2-Pulling is implemented through a “dummy particle” which moves towards
>>>> the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
>>>> and drags the CM by the harmonic force corresponding to the spring
>>>> constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
>>>> the PMF is averaged laterally
>>>>
>>>> 3-The conformations are scanned every 0.1 ps in order to save them
>>>> with the CM within each of the interval of width 0.05 nm. ( most of
>>>> all i'm not sure about this part of my mdp file and i don't know how
>>>> should i implement them).
>>>>
>>>> I don't know what .mdp setting you're referring to here.
>>>
>>> Sorry, I didn't understand what you mean?
>>>
>>
> The mailing list does not accept attachments, so your .mdp file did not
> come through. I'm working blind on what settings you're using. What I
> specifically don't understand here is your connection between the desired
> spacing along the reaction coordinate and whatever .mdp settings you think
> affect this. You can only tell mdrun how frequently to save a frame, you
> can't tell it anything about the interval along the reaction coordinate you
> care about. Save coordinates frequently enough that you can plausibly
> generate a set of configurations to use.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> ***@vt.edu | [phone]
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-***@gromacs.org.
>
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[Justin Lemkul]

On 11/25/17 3:07 PM, rose rahmani wrote:
> Oh sorry this is .mdp file:
>
> DEFINE = -DPOSRES

What are you restraining? This seems counterproductive, and by default
(unless you've hacked the topology), this is going to restrain your
protein, which is definitely wrong.

> integrator = md
> dt = 0.001
> nsteps = 2000000
> nstxout = 0
> nstvout = 0
> nstfout = 0
> nstlog = 500
> nstenergy = 1000
> nstxtcout = 1000
> rlist = 1.5
> rcoulomb = 1.5
> rvdw = 1.2

Again, I am suspicious of these cutoffs. What force field are you using?

> coulombtype = pme
> cutoff-scheme = group
> vdwtype = Switch
> rvdw_switch = 1.0
> pcoupl = no
> gen-vel = yes
> gen-temp = 0
> gen-seed = 173529
> constraints = h-bonds
> pbc = xy
> freezegrps = WAL ZnS
> freezedim = Y Y Y Y Y Y
> energygrp-excl = WAL WAL ZnO ZnO
> energygrps = SOL WAL ZnO Protein NA CL
> nwall = 2
> wall-atomtype = C C
> wall-type = 9-3
> wall-density = 150 150
> wall-ewald-zfac = 3
> ewald-geometry = 3dc
> fourierspacing = 0.12
> tcoupl = v-rescale
> tc-grps = System
> tau-t = 0.1
> ref-t = 300
> pull = yes
> pull_ngroups = 2
> pull_ncoords = 1
> pull_group1_name = ZnS
> pull_group2_name = Protein-H

You can probably just use the whole protein here, though I doubt it
makes much difference.

> pull_coord1_type = umbrella ; harmonic biasing force
> pull_coord1_geometry = distance ; simple distance increase
> pull_coord1_groups = 1 2
> pull_coord1_dim = N N Y
> pull_coord1_rate = 0.001

Here's your problem. With a positive pull rate, you are instructing
mdrun to increase the COM distance between the protein and the ZnS
surface. If you want them to come closer, you need a negative value
here, to decrease the distance as a function of time. Of course, this
all goes out the window if your protein is restrained, as suggested above.

-Justin

> pull_coord1_k = 5000 ; kJ mol^-1 nm^-2
> pull_coord1_start = yes ; define initial COM distance > 0
>
>
> On Sat, Nov 25, 2017 at 11:26 PM, Justin Lemkul <***@vt.edu> wrote:
>
>>
>> On 11/25/17 11:49 AM, rose rahmani wrote:
>>
>>> On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul <***@vt.edu> wrote:
>>>
>>>
>>>> On 11/24/17 3:32 PM, rose rahmani wrote:
>>>>
>>>> I attached md_pull.mdp file
>>>>> i put " cutoff-scheme = group" beecause of some errors (about energy
>>>>> groups)
>>>>>
>>>>> The use of energygrps has no effect on the physics. You should view
>>>> pairwise interactions energies as an analysis method, not something that
>>>> you need to do as part of your MD run. Don't base your algorithm choices
>>>> on
>>>> a quantity that is usually meaningless.
>>>>
>>>> This is what i try to do(part of some literatures);
>>>>
>>>>> 1-pulling the CM of the object along the z-axis—perpendicular to the
>>>>> surface of ZnO
>>>>>
>>>>> 2-Pulling is implemented through a “dummy particle” which moves towards
>>>>> the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
>>>>> and drags the CM by the harmonic force corresponding to the spring
>>>>> constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
>>>>> the PMF is averaged laterally
>>>>>
>>>>> 3-The conformations are scanned every 0.1 ps in order to save them
>>>>> with the CM within each of the interval of width 0.05 nm. ( most of
>>>>> all i'm not sure about this part of my mdp file and i don't know how
>>>>> should i implement them).
>>>>>
>>>>> I don't know what .mdp setting you're referring to here.
>>>> Sorry, I didn't understand what you mean?
>>>>
>> The mailing list does not accept attachments, so your .mdp file did not
>> come through. I'm working blind on what settings you're using. What I
>> specifically don't understand here is your connection between the desired
>> spacing along the reaction coordinate and whatever .mdp settings you think
>> affect this. You can only tell mdrun how frequently to save a frame, you
>> can't tell it anything about the interval along the reaction coordinate you
>> care about. Save coordinates frequently enough that you can plausibly
>> generate a set of configurations to use.
>>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> ***@vt.edu | [phone]
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-***@gromacs.org.
>>

--
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

***@vt.edu | [phone]
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================

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[rose rahmani]

On Sat, Nov 25, 2017 at 11:46 PM, Justin Lemkul <***@vt.edu> wrote:

>
>
> On 11/25/17 3:07 PM, rose rahmani wrote:
>
>> Oh sorry this is .mdp file:
>>
>> DEFINE = -DPOSRES
>>
>
> What are you restraining? This seems counterproductive, and by default
>> (unless you've hacked the topology), this is going to restrain your
>> protein, which is definitely wrong.
>
> yes, protein.you mean i should remove it and don't restraint anything? and
> for npt(previous step) run too?
>
>> integrator = md
>> dt = 0.001
>> nsteps = 2000000
>> nstxout = 0
>> nstvout = 0
>> nstfout = 0
>> nstlog = 500
>> nstenergy = 1000
>> nstxtcout = 1000
>> rlist = 1.5
>> rcoulomb = 1.5
>> rvdw = 1.2
>>
>
> Again, I am suspicious of these cutoffs. What force field are you using?
>
> AMBER99
>
> coulombtype = pme
>> cutoff-scheme = group
>> vdwtype = Switch
>> rvdw_switch = 1.0
>> pcoupl = no
>> gen-vel = yes
>> gen-temp = 0
>> gen-seed = 173529
>> constraints = h-bonds
>> pbc = xy
>> freezegrps = WAL ZnS
>> freezedim = Y Y Y Y Y Y
>> energygrp-excl = WAL WAL ZnO ZnO
>> energygrps = SOL WAL ZnO Protein NA CL
>> nwall = 2
>> wall-atomtype = C C
>> wall-type = 9-3
>> wall-density = 150 150
>> wall-ewald-zfac = 3
>> ewald-geometry = 3dc
>> fourierspacing = 0.12
>> tcoupl = v-rescale
>> tc-grps = System
>> tau-t = 0.1
>> ref-t = 300
>> pull = yes
>> pull_ngroups = 2
>> pull_ncoords = 1
>> pull_group1_name = ZnS
>> pull_group2_name = Protein-H
>>
>
> You can probably just use the whole protein here, though I doubt it makes
> much difference.
>
> pull_coord1_type = umbrella ; harmonic biasing force
>> pull_coord1_geometry = distance ; simple distance increase
>> pull_coord1_groups = 1 2
>> pull_coord1_dim = N N Y
>> pull_coord1_rate = 0.001
>>
>
> Here's your problem. With a positive pull rate, you are instructing mdrun
>> to increase the COM distance between the protein and the ZnS surface. If
>> you want them to come closer, you need a negative value here, to decrease
>> the distance as a function of time. Of course, this all goes out the window
>> if your protein is restrained, as suggested above.
>
>
oh, i've got it.
you restrained chain B in tutorial but i shouldn't because ZnS is freezed?


> -Justin
>
>
> pull_coord1_k = 5000 ; kJ mol^-1 nm^-2
>> pull_coord1_start = yes ; define initial COM distance > 0
>>
>>
>> On Sat, Nov 25, 2017 at 11:26 PM, Justin Lemkul <***@vt.edu> wrote:
>>
>>
>>> On 11/25/17 11:49 AM, rose rahmani wrote:
>>>
>>> On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul <***@vt.edu> wrote:
>>>>
>>>>
>>>> On 11/24/17 3:32 PM, rose rahmani wrote:
>>>>>
>>>>> I attached md_pull.mdp file
>>>>>
>>>>>> i put " cutoff-scheme = group" beecause of some errors (about energy
>>>>>> groups)
>>>>>>
>>>>>> The use of energygrps has no effect on the physics. You should view
>>>>>>
>>>>> pairwise interactions energies as an analysis method, not something
>>>>> that
>>>>> you need to do as part of your MD run. Don't base your algorithm
>>>>> choices
>>>>> on
>>>>> a quantity that is usually meaningless.
>>>>>
>>>>> This is what i try to do(part of some literatures);
>>>>>
>>>>> 1-pulling the CM of the object along the z-axis—perpendicular to the
>>>>>> surface of ZnO
>>>>>>
>>>>>> 2-Pulling is implemented through a “dummy particle” which moves
>>>>>> towards
>>>>>> the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0
>>>>>> and drags the CM by the harmonic force corresponding to the spring
>>>>>> constant of 5000 kJ/(mol nm2).The lateral motion is not constrained so
>>>>>> the PMF is averaged laterally
>>>>>>
>>>>>> 3-The conformations are scanned every 0.1 ps in order to save them
>>>>>> with the CM within each of the interval of width 0.05 nm. ( most of
>>>>>> all i'm not sure about this part of my mdp file and i don't know how
>>>>>> should i implement them).
>>>>>>
>>>>>> I don't know what .mdp setting you're referring to here.
>>>>>>
>>>>> Sorry, I didn't understand what you mean?
>>>>>
>>>>> The mailing list does not accept attachments, so your .mdp file did not
>>> come through. I'm working blind on what settings you're using. What I
>>> specifically don't understand here is your connection between the desired
>>> spacing along the reaction coordinate and whatever .mdp settings you
>>> think
>>> affect this. You can only tell mdrun how frequently to save a frame, you
>>> can't tell it anything about the interval along the reaction coordinate
>>> you
>>> care about. Save coordinates frequently enough that you can plausi
>>> <https://maps.google.com/?q=es+frequently+enough+that+you+can+plausi&entry=gmail&source=g>
>>> bly
>>> generate a set of configurations to use.
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> ***@vt.edu | [phone]
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-***@gromacs.org.
>>>
>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> ***@vt.edu | [phone]
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-***@gromacs.org.
>
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[Justin Lemkul]

On 11/25/17 3:59 PM, rose rahmani wrote:
> On Sat, Nov 25, 2017 at 11:46 PM, Justin Lemkul <***@vt.edu> wrote:
>
>>
>> On 11/25/17 3:07 PM, rose rahmani wrote:
>>
>>> Oh sorry this is .mdp file:
>>>
>>> DEFINE = -DPOSRES
>>>
>> What are you restraining? This seems counterproductive, and by default
>>> (unless you've hacked the topology), this is going to restrain your
>>> protein, which is definitely wrong.
>> yes, protein.you mean i should remove it and don't restraint anything? and
>> for npt(previous step) run too?

What is the purpose of a restraint? To prevent motion. What is your
objective? To cause motion of your protein towards a surface. Does it
make sense to restrain the protein during this process?

Equilibration is a separate matter.

>>> integrator = md
>>> dt = 0.001
>>> nsteps = 2000000
>>> nstxout = 0
>>> nstvout = 0
>>> nstfout = 0
>>> nstlog = 500
>>> nstenergy = 1000
>>> nstxtcout = 1000
>>> rlist = 1.5
>>> rcoulomb = 1.5
>>> rvdw = 1.2
>>>
>> Again, I am suspicious of these cutoffs. What force field are you using?
>>
>> AMBER99

Then yes, those cutoffs are wrong. This is also a very old force field,
and newer/better variants of it exist. Refer to the literature to find
the right cutoffs for the parameter set you decide upon. This is not a
trivial matter.

>> coulombtype = pme
>>> cutoff-scheme = group
>>> vdwtype = Switch
>>> rvdw_switch = 1.0
>>> pcoupl = no
>>> gen-vel = yes
>>> gen-temp = 0
>>> gen-seed = 173529
>>> constraints = h-bonds
>>> pbc = xy
>>> freezegrps = WAL ZnS
>>> freezedim = Y Y Y Y Y Y
>>> energygrp-excl = WAL WAL ZnO ZnO
>>> energygrps = SOL WAL ZnO Protein NA CL
>>> nwall = 2
>>> wall-atomtype = C C
>>> wall-type = 9-3
>>> wall-density = 150 150
>>> wall-ewald-zfac = 3
>>> ewald-geometry = 3dc
>>> fourierspacing = 0.12
>>> tcoupl = v-rescale
>>> tc-grps = System
>>> tau-t = 0.1
>>> ref-t = 300
>>> pull = yes
>>> pull_ngroups = 2
>>> pull_ncoords = 1
>>> pull_group1_name = ZnS
>>> pull_group2_name = Protein-H
>>>
>> You can probably just use the whole protein here, though I doubt it makes
>> much difference.
>>
>> pull_coord1_type = umbrella ; harmonic biasing force
>>> pull_coord1_geometry = distance ; simple distance increase
>>> pull_coord1_groups = 1 2
>>> pull_coord1_dim = N N Y
>>> pull_coord1_rate = 0.001
>>>
>> Here's your problem. With a positive pull rate, you are instructing mdrun
>>> to increase the COM distance between the protein and the ZnS surface. If
>>> you want them to come closer, you need a negative value here, to decrease
>>> the distance as a function of time. Of course, this all goes out the window
>>> if your protein is restrained, as suggested above.
>>
> oh, i've got it.
> you restrained chain B in tutorial but i shouldn't because ZnS is freezed?

No, I restrained a chain in my protein to mimic the stability of
(physiologically) much larger systems. People typically fail to read my
paper that is the basis of that tutorial, in which this concept is
explained. Perhaps I need to add a bold, flashing warning that people
should not be blindly following the method.

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

***@vt.edu | [phone]
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================

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[rose rahmani]

Hello;

I took 2000 configuration from trajconv. Amino acid is in its normal shape
till almost conf1000.gro(and a little more). But in for example
conf1300.gro amino acid was disintegrated. What does it mean? Would you
please help me?

Best regards
Rose

On Sun, Nov 26, 2017 at 12:39 AM, Justin Lemkul <***@vt.edu> wrote:

>
>
> On 11/25/17 3:59 PM, rose rahmani wrote:
>
>> On Sat, Nov 25, 2017 at 11:46 PM, Justin Lemkul <***@vt.edu> wrote:
>>
>>
>>> On 11/25/17 3:07 PM, rose rahmani wrote:
>>>
>>> Oh sorry this is .mdp file:
>>>>
>>>> DEFINE = -DPOSRES
>>>>
>>>> What are you restraining? This seems counterproductive, and by default
>>>
>>>> (unless you've hacked the topology), this is going to restrain your
>>>> protein, which is definitely wrong.
>>>>
>>> yes, protein.you mean i should remove it and don't restraint anything?
>>> and
>>> for npt(previous step) run too?
>>>
>>
> What is the purpose of a restraint? To prevent motion. What is your
> objective? To cause motion of your protein towards a surface. Does it make
> sense to restrain the protein during this process?
>
> Equilibration is a separate matter.
>
> integrator = md
>>>> dt = 0.001
>>>> nsteps = 2000000
>>>> nstxout = 0
>>>> nstvout = 0
>>>> nstfout = 0
>>>> nstlog = 500
>>>> nstenergy = 1000
>>>> nstxtcout = 1000
>>>> rlist = 1.5
>>>> rcoulomb = 1.5
>>>> rvdw = 1.2
>>>>
>>>> Again, I am suspicious of these cutoffs. What force field are you using?
>>>
>>> AMBER99
>>>
>>
> Then yes, those cutoffs are wrong. This is also a very old force field,
> and newer/better variants of it exist. Refer to the literature to find the
> right cutoffs for the parameter set you decide upon. This is not a trivial
> matter.
>
>
> coulombtype = pme
>>>
>>>> cutoff-scheme = group
>>>> vdwtype = Switch
>>>> rvdw_switch = 1.0
>>>> pcoupl = no
>>>> gen-vel = yes
>>>> gen-temp = 0
>>>> gen-seed = 173529
>>>> constraints = h-bonds
>>>> pbc = xy
>>>> freezegrps = WAL ZnS
>>>> freezedim = Y Y Y Y Y Y
>>>> energygrp-excl = WAL WAL ZnO ZnO
>>>> energygrps = SOL WAL ZnO Protein NA CL
>>>> nwall = 2
>>>> wall-atomtype = C C
>>>> wall-type = 9-3
>>>> wall-density = 150 150
>>>> wall-ewald-zfac = 3
>>>> ewald-geometry = 3dc
>>>> fourierspacing = 0.12
>>>> tcoupl = v-rescale
>>>> tc-grps = System
>>>> tau-t = 0.1
>>>> ref-t = 300
>>>> pull = yes
>>>> pull_ngroups = 2
>>>> pull_ncoords = 1
>>>> pull_group1_name = ZnS
>>>> pull_group2_name = Protein-H
>>>>
>>>> You can probably just use the whole protein here, though I doubt it
>>> makes
>>> much difference.
>>>
>>> pull_coord1_type = umbrella ; harmonic biasing force
>>>
>>>> pull_coord1_geometry = distance ; simple distance increase
>>>> pull_coord1_groups = 1 2
>>>> pull_coord1_dim = N N Y
>>>> pull_coord1_rate = 0.001
>>>>
>>>> Here's your problem. With a positive pull rate, you are instructing
>>> mdrun
>>>
>>>> to increase the COM distance between the protein and the ZnS surface. If
>>>> you want them to come closer, you need a negative value here, to
>>>> decrease
>>>> the distance as a function of time. Of course, this all goes out the
>>>> window
>>>> if your protein is restrained, as suggested above.
>>>>
>>>
>>> oh, i've got it.
>> you restrained chain B in tutorial but i shouldn't because ZnS is freezed?
>>
>
> No, I restrained a chain in my protein to mimic the stability of
> (physiologically) much larger systems. People typically fail to read my
> paper that is the basis of that tutorial, in which this concept is
> explained. Perhaps I need to add a bold, flashing warning that people
> should not be blindly following the method.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> ***@vt.edu | [phone]
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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[Justin Lemkul]

On 11/28/17 12:23 AM, rose rahmani wrote:
> Hello;
>
> I took 2000 configuration from trajconv. Amino acid is in its normal shape
> till almost conf1000.gro(and a little more). But in for example
> conf1300.gro amino acid was disintegrated. What does it mean? Would you
> please help me?

Bonds can't break and molecules can't "disintegrate" - what you're
seeing is probably a result of PBC.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

***@vt.edu | [phone]
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================

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[rose rahmani]

Would "pull_geometry=periodic-distance" be another solution for it?

On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul <***@vt.edu> wrote:

>
>
> On 11/28/17 12:23 AM, rose rahmani wrote:
>
>> Hello;
>>
>> I took 2000 configuration from trajconv. Amino acid is in its normal shape
>> till almost conf1000.gro(and a little more). But in for example
>> conf1300.gro amino acid was disintegrated. What does it mean? Would you
>> please help me?
>>
>
> Bonds can't break and molecules can't "disintegrate" - what you're seeing
> is probably a result of PBC.
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_
> Boundary_Conditions
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> ***@vt.edu | [phone]
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-***@gromacs.org.
>
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[Justin Lemkul]

On 11/28/17 10:00 AM, rose rahmani wrote:
> Would "pull_geometry=periodic-distance" be another solution for it?

No. That affects how the reaction coordinate distance is calculated, not
the PBC treatment, which is intrinsic to any simulation using PBC.

-Justin

> On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul <***@vt.edu> wrote:
>
>>
>> On 11/28/17 12:23 AM, rose rahmani wrote:
>>
>>> Hello;
>>>
>>> I took 2000 configuration from trajconv. Amino acid is in its normal shape
>>> till almost conf1000.gro(and a little more). But in for example
>>> conf1300.gro amino acid was disintegrated. What does it mean? Would you
>>> please help me?
>>>
>> Bonds can't break and molecules can't "disintegrate" - what you're seeing
>> is probably a result of PBC.
>>
>> http://www.gromacs.org/Documentation/Terminology/Periodic_
>> Boundary_Conditions
>>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> ***@vt.edu | [phone]
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>> send a mail to gmx-users-***@gromacs.org.
>>

--
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

***@vt.edu | [phone]
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================

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[rose rahmani]

On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul <***@vt.edu> wrote:

>
>
> On 11/28/17 12:23 AM, rose rahmani wrote:
>
>> Hello;
>>
>> I took 2000 configuration from trajconv. Amino acid is in its normal shape
>> till almost conf1000.gro(and a little more). But in for example
>> conf1300.gro amino acid was disintegrated. What does it mean? Would you
>> please help me?
>>
>
> Bonds can't break and molecules can't "disintegrate" - what you're seeing
> is probably a result of PBC.
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_
>> Boundary_Conditions
>
> I don't know why this doesn't work since yesterday?!!!!...anyway...
>
I used trjconv for just one frame for example conf2000;
trjconv -f conf2000.gro -n index.ndx -s pull.tpr -o new_conf2000.gro -pbc
whole

so protein turned into to its normal shape, but i'm not sure does it makes
sense or not?! is that right? if it's right, another problem is;
protein is getting out of box, should i use trjconv for centering?

Thank you for your attentions


>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> ***@vt.edu | [phone]
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-***@gromacs.org.
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[rose rahmani]

I need to share you sth which just happened;
i run md_pull.mdp in two steps:
1--1nS( dt= 0.001 nsteps=1000000) ,
2--then i choosed last frame (conf1000.gro) and run it irst time for 2nS(
dt= 0.001 nsteps=2000000) and scond time for 4nS (dt=0.001 nsteps=4000000)
and The protein was in normal shape in EVERY steps!

BUT as i told you before when i run just once in 2nS (dt=0.001
nsteps=2000000) periodic boundary conditions make the protein look unusual
in for example conf1500.gro?!!!
What happened? I've got really confused?

Thank ou for your attentions

-Rose


On Sun, Dec 3, 2017 at 4:31 PM, rose rahmani <***@gmail.com> wrote:

>
>
> On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul <***@vt.edu> wrote:
>
>>
>>
>> On 11/28/17 12:23 AM, rose rahmani wrote:
>>
>>> Hello;
>>>
>>> I took 2000 configuration from trajconv. Amino acid is in its normal
>>> shape
>>> till almost conf1000.gro(and a little more). But in for example
>>> conf1300.gro amino acid was disintegrated. What does it mean? Would you
>>> please help me?
>>>
>>
>> Bonds can't break and molecules can't "disintegrate" - what you're seeing
>> is probably a result of PBC.
>>
>> http://www.gromacs.org/Documentation/Terminology/Periodic_Bo
>>> undary_Conditions
>>
>> I don't know why this doesn't work since yesterday?!!!!...anyway...
>>
> I used trjconv for just one frame for example conf2000;
> trjconv -f conf2000.gro -n index.ndx -s pull.tpr -o new_conf2000.gro -pbc
> whole
>
> so protein turned into to its normal shape, but i'm not sure does it makes
> sense or not?! is that right? if it's right, another problem is;
> protein is getting out of box, should i use trjconv for centering?
>
> Thank you for your attentions
>
>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> ***@vt.edu | [phone]
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-***@gromacs.org.
>>
>
>
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[Justin Lemkul]

On 12/3/17 8:42 AM, rose rahmani wrote:
> I need to share you sth which just happened;
> i run md_pull.mdp in two steps:
> 1--1nS( dt= 0.001 nsteps=1000000) ,
> 2--then i choosed last frame (conf1000.gro) and run it irst time for 2nS(
> dt= 0.001 nsteps=2000000) and scond time for 4nS (dt=0.001 nsteps=4000000)
> and The protein was in normal shape in EVERY steps!
>
> BUT as i told you before when i run just once in 2nS (dt=0.001
> nsteps=2000000) periodic boundary conditions make the protein look unusual
> in for example conf1500.gro?!!!
> What happened? I've got really confused?

Read a bit about periodic boundary conditions and what they mean. This
is normal behavior.

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

***@vt.edu | [phone]
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================

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[rose rahmani]

Hi,

I try to use umbrella sampling for calculating PMF. i change distance
between protein and ZNS nanosheet. I use gomacsV4.5.4

after minimization and equilibration. i use:

grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -o pull.tpr

this is md_pull.mdp:

integrator = md
dt = 0.002
nsteps = 1000000
nstxout = 5000
nstvout = 5000
nstfout = 500
nstlog = 500
nstenergy = 1000
nstxtcout = 1000
nstlist = 10
rlist = 1.5
coulombtype = pme
rcoulomb = 1.5
vdwtype = Switch
rvdw_switch = 1.0
rvdw = 1.2
pcoupl = no
gen_vel = no
constraints = h-bonds
ns_type = grid
pbc = xy
freezegrps = WAL ZnS
freezedim = Y Y Y Y Y Y
energygrp-excl = WAL WAL ZnS ZnS
energygrps = SOL WAL ZnS Protein NA CL
nwall = 2
wall-atomtype = C C
wall-type = 9-3
wall-density = 150 150
wall-ewald-zfac = 3
ewald-geometry = 3dc
fourierspacing = 0.12
tcoupl = v-rescale
tc-grps = System
tau-t = 0.1
ref-t = 300

; Pull code
pull = umbrella
pull_ngroups = 1
pull_group0 = ZnS
pull_group1 = Protein
pull_geometry = direction
pull_vec1 = 0 0 1
pull_dim = N N Y
pull_rate1 = -0.01
pull_k1 = 5000
pull_start = yes
pull_nstxout = 50

then: mdrun -s pull.tpr
then:trjconv -s pull.tpr -f traj_comp.xtc -o conf.gro -sep

i got 1000 configuration, i selected 27 of them and foe each of them i run
md_umbrella.mdp

for example: grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top
-n index.ndx -o umbrella0.tpr and then:

mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg


.This is md_umbrella.mdp file:

ntegrator = md
dt = 0.002
nsteps = 2000000
nstxout = 5000
nstvout = 5000
nstfout = 500
nstlog = 500
nstenergy = 1000
nstxtcout = 1000
nstlist = 10
rlist = 1.5
coulombtype = pme
rcoulomb = 1.5
vdwtype = Switch
rvdw_switch = 1.0
rvdw = 1.2
pcoupl = no
gen_vel = no
constraints = h-bonds
ns_type = grid
pbc = xy
freezegrps = WAL ZnS
freezedim = Y Y Y Y Y Y
energygrp-excl = WAL WAL ZnS ZnS
energygrps = SOL WAL ZnS Protein NA CL
nwall = 2
wall-atomtype = C C
wall-type = 9-3
wall-density = 150 150
wall-ewald-zfac = 3
ewald-geometry = 3dc
fourierspacing = 0.12
tcoupl = v-rescale
tc-grps = System
tau-t = 0.1
ref-t = 300

pull = umbrella
pull_ngroups = 1
pull_group0 = ZnS
pull_group1 = Protein
pull_geometry = direction
pull_vec1 = 0 0 1
pull_dim = N N Y
pull_rate1 = 0.0 ; 1 nm per ns
pull_k1 = 5000
pull_start = yes
pull_nstxout = 50
...........................................................

then i use :

wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal


i get histo.xvg and profile.xvg file but the profile.xvg contains nan
vavlue. i don't know why?


# This file was created Wed Dec 13 14:54:35 2017 # by the following
command: # g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
# # g_wham is part of G R O M A C S: # # GROwing Monsters And Cloning
Shrimps # @ title "Umbrella potential" @ xaxis label "z" @ yaxis label "E
(kcal mol\S-1\N)" @TYPE xy 5.723834e-01 -nan 6.714198e-01 -nan 7.704562e-01
-nan 8.694925e-01 -nan 9.685289e-01 -nan 1.067565e+00 -nan 1.166602e+00
-nan 1.265638e+00 -nan

.

.

.

.


Would you please help me? i have not encounter this problem before

Thank you so much

Best regards

Rose




On Mon, Dec 4, 2017 at 1:55 AM, Justin Lemkul <***@vt.edu> wrote:

>
>
> On 12/3/17 8:42 AM, rose rahmani wrote:
>
>> I need to share you sth which just happened;
>> i run md_pull.mdp in two steps:
>> 1--1nS( dt= 0.001 nsteps=1000000) ,
>> 2--then i choosed last frame (conf1000.gro) and run it irst time for
>> 2nS(
>> dt= 0.001 nsteps=2000000) and scond time for 4nS (dt=0.001 nsteps=4000000)
>> and The protein was in normal shape in EVERY steps!
>>
>> BUT as i told you before when i run just once in 2nS (dt=0.001
>> nsteps=2000000) periodic boundary conditions make the protein look unusual
>> in for example conf1500.gro?!!!
>> What happened? I've got really confused?
>>
>
> Read a bit about periodic boundary conditions and what they mean. This is
> normal behavior.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> ***@vt.edu | [phone]
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-***@gromacs.org.
>
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[rose rahmani]

and also i want protein get closer to ZnS sheet during pulling in just Z
direction and straightforward to sheet( like one straight line to sheet),
is this suitable md_pull.mdp file for this approach? and what about time?is
4nS suitable for each window?

Thanks indeed

On Sat, Dec 16, 2017 at 10:05 AM, rose rahmani <***@gmail.com>
wrote:

> Hi,
>
> I try to use umbrella sampling for calculating PMF. i change distance
> between protein and ZNS nanosheet. I use gomacsV4.5.4
>
> after minimization and equilibration. i use:
>
> grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -o pull.tpr
>
> this is md_pull.mdp:
>
> integrator = md
> dt = 0.002
> nsteps = 1000000
> nstxout = 5000
> nstvout = 5000
> nstfout = 500
> nstlog = 500
> nstenergy = 1000
> nstxtcout = 1000
> nstlist = 10
> rlist = 1.5
> coulombtype = pme
> rcoulomb = 1.5
> vdwtype = Switch
> rvdw_switch = 1.0
> rvdw = 1.2
> pcoupl = no
> gen_vel = no
> constraints = h-bonds
> ns_type = grid
> pbc = xy
> freezegrps = WAL ZnS
> freezedim = Y Y Y Y Y Y
> energygrp-excl = WAL WAL ZnS ZnS
> energygrps = SOL WAL ZnS Protein NA CL
> nwall = 2
> wall-atomtype = C C
> wall-type = 9-3
> wall-density = 150 150
> wall-ewald-zfac = 3
> ewald-geometry = 3dc
> fourierspacing = 0.12
> tcoupl = v-rescale
> tc-grps = System
> tau-t = 0.1
> ref-t = 300
>
> ; Pull code
> pull = umbrella
> pull_ngroups = 1
> pull_group0 = ZnS
> pull_group1 = Protein
> pull_geometry = direction
> pull_vec1 = 0 0 1
> pull_dim = N N Y
> pull_rate1 = -0.01
> pull_k1 = 5000
> pull_start = yes
> pull_nstxout = 50
>
> then: mdrun -s pull.tpr
> then:trjconv -s pull.tpr -f traj_comp.xtc -o conf.gro -sep
>
> i got 1000 configuration, i selected 27 of them and foe each of them i run
> md_umbrella.mdp
>
> for example: grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p
> topol.top -n index.ndx -o umbrella0.tpr and then:
>
> mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg
>
>
> .This is md_umbrella.mdp file:
>
> ntegrator = md
> dt = 0.002
> nsteps = 2000000
> nstxout = 5000
> nstvout = 5000
> nstfout = 500
> nstlog = 500
> nstenergy = 1000
> nstxtcout = 1000
> nstlist = 10
> rlist = 1.5
> coulombtype = pme
> rcoulomb = 1.5
> vdwtype = Switch
> rvdw_switch = 1.0
> rvdw = 1.2
> pcoupl = no
> gen_vel = no
> constraints = h-bonds
> ns_type = grid
> pbc = xy
> freezegrps = WAL ZnS
> freezedim = Y Y Y Y Y Y
> energygrp-excl = WAL WAL ZnS ZnS
> energygrps = SOL WAL ZnS Protein NA CL
> nwall = 2
> wall-atomtype = C C
> wall-type = 9-3
> wall-density = 150 150
> wall-ewald-zfac = 3
> ewald-geometry = 3dc
> fourierspacing = 0.12
> tcoupl = v-rescale
> tc-grps = System
> tau-t = 0.1
> ref-t = 300
>
> pull = umbrella
> pull_ngroups = 1
> pull_group0 = ZnS
> pull_group1 = Protein
> pull_geometry = direction
> pull_vec1 = 0 0 1
> pull_dim = N N Y
> pull_rate1 = 0.0 ; 1 nm per ns
> pull_k1 = 5000
> pull_start = yes
> pull_nstxout = 50
> ...........................................................
>
> then i use :
>
> wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
>
>
> i get histo.xvg and profile.xvg file but the profile.xvg contains nan vavlue. i don't know why?
>
>
> # This file was created Wed Dec 13 14:54:35 2017 # by the following
> command: # g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
> # # g_wham is part of G R O M A C S: # # GROwing Monsters And Cloning
> Shrimps # @ title "Umbrella potential" @ xaxis label "z" @ yaxis label "E
> (kcal mol\S-1\N)" @TYPE xy 5.723834e-01 -nan 6.714198e-01 -nan 7.704562e-01
> -nan 8.694925e-01 -nan 9.685289e-01 -nan 1.067565e+00 -nan 1.166602e+00
> -nan 1.265638e+00 -nan
>
> .
>
> .
>
> .
>
> .
>
>
> Would you please help me? i have not encounter this problem before
>
> Thank you so much
>
> Best regards
>
> Rose
>
>
>
>
> On Mon, Dec 4, 2017 at 1:55 AM, Justin Lemkul <***@vt.edu> wrote:
>
>>
>>
>> On 12/3/17 8:42 AM, rose rahmani wrote:
>>
>>> I need to share you sth which just happened;
>>> i run md_pull.mdp in two steps:
>>> 1--1nS( dt= 0.001 nsteps=1000000) ,
>>> 2--then i choosed last frame (conf1000.gro) and run it irst time for
>>> 2nS(
>>> dt= 0.001 nsteps=2000000) and scond time for 4nS (dt=0.001
>>> nsteps=4000000)
>>> and The protein was in normal shape in EVERY steps!
>>>
>>> BUT as i told you before when i run just once in 2nS (dt=0.001
>>> nsteps=2000000) periodic boundary conditions make the protein look
>>> unusual
>>> in for example conf1500.gro?!!!
>>> What happened? I've got really confused?
>>>
>>
>> Read a bit about periodic boundary conditions and what they mean. This is
>> normal behavior.
>>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> ***@vt.edu | [phone]
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-***@gromacs.org.
>>
>
>
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[rose rahmani]

On Sat, Dec 16, 2017 at 12:38 PM, rose rahmani <***@gmail.com>
wrote:

> and also i want protein get closer to ZnS sheet during pulling in just Z
>> direction and straightforward to sheet( like one straight line to sheet),
>> is this suitable md_pull.mdp file for this approach?
>
> is it possible at all?1

> and what about time?is 4nS suitable for each window?
>
>
> Thanks indeed
>
> On Sat, Dec 16, 2017 at 10:05 AM, rose rahmani <***@gmail.com>
> wrote:
>
>> Hi,
>>
>> I try to use umbrella sampling for calculating PMF. i change distance
>> between protein and ZNS nanosheet. I use gomacsV4.5.4
>>
>> after minimization and equilibration. i use:
>>
>> grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -o pull.tpr
>>
>> this is md_pull.mdp:
>>
>> integrator = md
>> dt = 0.002
>> nsteps = 1000000
>> nstxout = 5000
>> nstvout = 5000
>> nstfout = 500
>> nstlog = 500
>> nstenergy = 1000
>> nstxtcout = 1000
>> nstlist = 10
>> rlist = 1.5
>> coulombtype = pme
>> rcoulomb = 1.5
>> vdwtype = Switch
>> rvdw_switch = 1.0
>> rvdw = 1.2
>> pcoupl = no
>> gen_vel = no
>> constraints = h-bonds
>> ns_type = grid
>> pbc = xy
>> freezegrps = WAL ZnS
>> freezedim = Y Y Y Y Y Y
>> energygrp-excl = WAL WAL ZnS ZnS
>> energygrps = SOL WAL ZnS Protein NA CL
>> nwall = 2
>> wall-atomtype = C C
>> wall-type = 9-3
>> wall-density = 150 150
>> wall-ewald-zfac = 3
>> ewald-geometry = 3dc
>> fourierspacing = 0.12
>> tcoupl = v-rescale
>> tc-grps = System
>> tau-t = 0.1
>> ref-t = 300
>>
>> ; Pull code
>> pull = umbrella
>> pull_ngroups = 1
>> pull_group0 = ZnS
>> pull_group1 = Protein
>> pull_geometry = direction
>> pull_vec1 = 0 0 1
>> pull_dim = N N Y
>> pull_rate1 = -0.01
>> pull_k1 = 5000
>> pull_start = yes
>> pull_nstxout = 50
>>
>> then: mdrun -s pull.tpr
>> then:trjconv -s pull.tpr -f traj_comp.xtc -o conf.gro -sep
>>
>> i got 1000 configuration, i selected 27 of them and foe each of them i
>> run md_umbrella.mdp
>>
>> for example: grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p
>> topol.top -n index.ndx -o umbrella0.tpr and then:
>>
>> mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg
>>
>>
>> .This is md_umbrella.mdp file:
>>
>> ntegrator = md
>> dt = 0.002
>> nsteps = 2000000
>> nstxout = 5000
>> nstvout = 5000
>> nstfout = 500
>> nstlog = 500
>> nstenergy = 1000
>> nstxtcout = 1000
>> nstlist = 10
>> rlist = 1.5
>> coulombtype = pme
>> rcoulomb = 1.5
>> vdwtype = Switch
>> rvdw_switch = 1.0
>> rvdw = 1.2
>> pcoupl = no
>> gen_vel = no
>> constraints = h-bonds
>> ns_type = grid
>> pbc = xy
>> freezegrps = WAL ZnS
>> freezedim = Y Y Y Y Y Y
>> energygrp-excl = WAL WAL ZnS ZnS
>> energygrps = SOL WAL ZnS Protein NA CL
>> nwall = 2
>> wall-atomtype = C C
>> wall-type = 9-3
>> wall-density = 150 150
>> wall-ewald-zfac = 3
>> ewald-geometry = 3dc
>> fourierspacing = 0.12
>> tcoupl = v-rescale
>> tc-grps = System
>> tau-t = 0.1
>> ref-t = 300
>>
>> pull = umbrella
>> pull_ngroups = 1
>> pull_group0 = ZnS
>> pull_group1 = Protein
>> pull_geometry = direction
>> pull_vec1 = 0 0 1
>> pull_dim = N N Y
>> pull_rate1 = 0.0 ; 1 nm per ns
>> pull_k1 = 5000
>> pull_start = yes
>> pull_nstxout = 50
>> ...........................................................
>>
>> then i use :
>>
>> wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
>>
>>
>> i get histo.xvg and profile.xvg file but the profile.xvg contains nan vavlue. i don't know why?
>>
>>
>> # This file was created Wed Dec 13 14:54:35 2017 # by the following
>> command: # g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
>> # # g_wham is part of G R O M A C S: # # GROwing Monsters And Cloning
>> Shrimps # @ title "Umbrella potential" @ xaxis label "z" @ yaxis label "E
>> (kcal mol\S-1\N)" @TYPE xy 5.723834e-01 -nan 6.714198e-01 -nan 7.704562e-01
>> -nan 8.694925e-01 -nan 9.685289e-01 -nan 1.067565e+00 -nan 1.166602e+00
>> -nan 1.265638e+00 -nan
>>
>> .
>>
>> .
>>
>> .
>>
>> .
>>
>>
>> Would you please help me? i have not encounter this problem before
>>
>> Thank you so much
>>
>> Best regards
>>
>> Rose
>>
>>
>>
>>
>> On Mon, Dec 4, 2017 at 1:55 AM, Justin Lemkul <***@vt.edu> wrote:
>>
>>>
>>>
>>> On 12/3/17 8:42 AM, rose rahmani wrote:
>>>
>>>> I need to share you sth which just happened;
>>>> i run md_pull.mdp in two steps:
>>>> 1--1nS( dt= 0.001 nsteps=1000000) ,
>>>> 2--then i choosed last frame (conf1000.gro) and run it irst time for
>>>> 2nS(
>>>> dt= 0.001 nsteps=2000000) and scond time for 4nS (dt=0.001
>>>> nsteps=4000000)
>>>> and The protein was in normal shape in EVERY steps!
>>>>
>>>> BUT as i told you before when i run just once in 2nS (dt=0.001
>>>> nsteps=2000000) periodic boundary conditions make the protein look
>>>> unusual
>>>> in for example conf1500.gro?!!!
>>>> What happened? I've got really confused?
>>>>
>>>
>>> Read a bit about periodic boundary conditions and what they mean. This
>>> is normal behavior.
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> ***@vt.edu | [phone]
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
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>>>
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>>> send a mail to gmx-users-***@gromacs.org.
>>>
>>
>>
>
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[Justin Lemkul]

On 12/3/17 8:01 AM, rose rahmani wrote:
> On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul <***@vt.edu> wrote:
>
>>
>> On 11/28/17 12:23 AM, rose rahmani wrote:
>>
>>> Hello;
>>>
>>> I took 2000 configuration from trajconv. Amino acid is in its normal shape
>>> till almost conf1000.gro(and a little more). But in for example
>>> conf1300.gro amino acid was disintegrated. What does it mean? Would you
>>> please help me?
>>>
>> Bonds can't break and molecules can't "disintegrate" - what you're seeing
>> is probably a result of PBC.
>>
>> http://www.gromacs.org/Documentation/Terminology/Periodic_
>>> Boundary_Conditions
>> I don't know why this doesn't work since yesterday?!!!!...anyway...
>>
> I used trjconv for just one frame for example conf2000;
> trjconv -f conf2000.gro -n index.ndx -s pull.tpr -o new_conf2000.gro -pbc
> whole
>
> so protein turned into to its normal shape, but i'm not sure does it makes
> sense or not?! is that right? if it's right, another problem is;
> protein is getting out of box, should i use trjconv for centering?
>
> Thank you for your attentions

A "whole" molecule only matters for visualization. It has no impact on
physical interactions computed by mdrun.

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

***@vt.edu | [phone]
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================

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[s***@iacs.res.in]

Hi all
I am doing umbrella sampling taking distance between COM as a reaction
coordinate. when I am trying to calculate PMF using the following command
 gmx wham -it tpr-files.dat -if pullf-files.dat  -o free.xvg -hist
hist.xvg
I got an error 

Program:     gmx wham, version 2016.3
Source file: src/gromacs/gmxana/gmx_wham.cpp (line 1821)
 
Fatal error:
Unknown file type of . Should be tpr, xvg, or pdo.

my tpr-files.dat is 

umbrella0.tpr
umbrella1.tpr
umbrella2.tpr
umbrella3.tpr
umbrella4.tpr
umbrella5.tpr
umbrella6.tpr
umbrella7.tpr
umbrella8.tpr
umbrella9.tpr
umbrella10.tpr
umbrella11.tpr
umbrella12.tpr

and pullf-files.dat is

pullf0.xvg
pullf1.xvg
pullf2.xvg
pullf3.xvg
pullf4.xvg
pullf5.xvg
pullf6.xvg
pullf7.xvg
pullf8.xvg
pullf9.xvg
pullf10.xvg
pullf11.xvg
pullf12.xvg
 

And I am using gromacs-2016.3. Can anyone suggest me something?
Thanks
Sunipa 
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[Dhaniram Mahato]

Hi,

There could be format problem. You can create your own .dat files by typing
it. You have probably copied it from somewhere. I hope it will work then.

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html

Thanks
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[s***@iacs.res.in]

----- Message from Dhaniram Mahato <***@gmail.com> ---------
    Date: Tue, 19 Dec 2017 21:30:05 +0800
    From: Dhaniram Mahato <***@gmail.com>
Reply-To: gmx-***@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
      To: gmx-***@gromacs.org

> Hi,
>
> There could be format problem. You can create your own .dat files by
> typing
> it. You have probably copied it from somewhere. I hope it will work then.
>
>
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html
>
> Thanks
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> or send a mail to gmx-users-***@gromacs.org.

Hii
Thanks for replying. I have prepared it by own.I have not copied it.

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[s***@iacs.res.in]

----- Message from Dhaniram Mahato <***@gmail.com> ---------
    Date: Tue, 19 Dec 2017 21:30:05 +0800
    From: Dhaniram Mahato <***@gmail.com>
Reply-To: gmx-***@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
      To: gmx-***@gromacs.org

> Hi,
>
> There could be format problem. You can create your own .dat files by
> typing
> it. You have probably copied it from somewhere. I hope it will work then.
>
>
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html
>
> Thanks
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests
> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or send a mail to gmx-users-***@gromacs.org.

Hii
I have solved the problem. It was just because of one extra space added in
the tpr-files.dat file. Now its running properly.

----- End message from Dhaniram Mahato <***@gmail.com> -----
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[Jefferies D.F.]

Out of curiosity, how did you manage to identify and subsequently remove the extra space? I have been having similar problems and the tools I've used haven't fixed this problem.

Thanks,
________________________________________
From: gromacs.org_gmx-users-***@maillist.sys.kth.se [gromacs.org_gmx-users-***@maillist.sys.kth.se] on behalf of ***@iacs.res.in [***@iacs.res.in]
Sent: Tuesday, December 19, 2017 6:21 PM
To: gromacs.org_gmx-***@maillist.sys.kth.se
Subject: Re: [gmx-users] Umbrella sampling

----- Message from Dhaniram Mahato <***@gmail.com> ---------
Date: Tue, 19 Dec 2017 21:30:05 +0800
From: Dhaniram Mahato <***@gmail.com>
Reply-To: gmx-***@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
To: gmx-***@gromacs.org

> Hi,
>
> There could be format problem. You can create your own .dat files by
> typing
> it. You have probably copied it from somewhere. I hope it will work then.
>
>
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html
>
> Thanks
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or send a mail to gmx-users-***@gromacs.org.

Hii
I have solved the problem. It was just because of one extra space added in
the tpr-files.dat file. Now its running properly.

----- End message from Dhaniram Mahato <***@gmail.com> -----
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[Mark Abraham]

Hi,

Yes, the parsing of that file looks like it doesn't handle blank lines
gracefully, at least. Use a text editor and clean things up. And make sure
the file endings are unix style, e.g. with dos2unix if relevant.

Mark

On Wed, Dec 20, 2017 at 7:57 AM Jefferies D.F. <***@soton.ac.uk> wrote:

> Out of curiosity, how did you manage to identify and subsequently remove
> the extra space? I have been having similar problems and the tools I've
> used haven't fixed this problem.
>
> Thanks,
> ________________________________________
> From: gromacs.org_gmx-users-***@maillist.sys.kth.se [
> gromacs.org_gmx-users-***@maillist.sys.kth.se] on behalf of
> ***@iacs.res.in [***@iacs.res.in]
> Sent: Tuesday, December 19, 2017 6:21 PM
> To: gromacs.org_gmx-***@maillist.sys.kth.se
> Subject: Re: [gmx-users] Umbrella sampling
>
> ----- Message from Dhaniram Mahato <***@gmail.com> ---------
> Date: Tue, 19 Dec 2017 21:30:05 +0800
> From: Dhaniram Mahato <***@gmail.com>
> Reply-To: gmx-***@gromacs.org
> Subject: Re: [gmx-users] Umbrella sampling
> To: gmx-***@gromacs.org
>
> > Hi,
> >
> > There could be format problem. You can create your own .dat files by
> > typing
> > it. You have probably copied it from somewhere. I hope it will work then.
> >
> >
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html
> >
> > Thanks
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests
> > visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or send a mail to gmx-users-***@gromacs.org.
>
> Hii
> I have solved the problem. It was just because of one extra space added in
> the tpr-files.dat file. Now its running properly.
>
> ----- End message from Dhaniram Mahato <***@gmail.com> -----
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[s***@iacs.res.in]

----- Message from Mark Abraham <***@gmail.com> ---------
    Date: Fri, 22 Dec 2017 00:42:31 +0000
    From: Mark Abraham <***@gmail.com>
Reply-To: gmx-***@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
      To: gmx-***@gromacs.org
      Cc: gromacs.org_gmx-***@maillist.sys.kth.se

> Hi,
>
> Yes, the parsing of that file looks like it doesn't handle blank lines
> gracefully, at least. Use a text editor and clean things up. And make
sure
> the file endings are unix style, e.g. with dos2unix if relevant.
>
> Mark
>
> On Wed, Dec 20, 2017 at 7:57 AM Jefferies D.F. <***@soton.ac.uk>
> wrote:
>
>> Out of curiosity, how did you manage to identify and subsequently remove
>> the extra space? I have been having similar problems and the tools I've
>> used haven't fixed this problem.
>>
>> Thanks,
>> ________________________________________
>> From: gromacs.org_gmx-users-***@maillist.sys.kth.se [
>> gromacs.org_gmx-users-***@maillist.sys.kth.se] on behalf of
>> ***@iacs.res.in [***@iacs.res.in]
>> Sent: Tuesday, December 19, 2017 6:21 PM
>> To: gromacs.org_gmx-***@maillist.sys.kth.se
>> Subject: Re: [gmx-users] Umbrella sampling
>>
>>   ----- Message from Dhaniram Mahato <***@gmail.com> ---------
>>     Date: Tue, 19 Dec 2017 21:30:05 +0800
>>     From: Dhaniram Mahato <***@gmail.com>
>> Reply-To: gmx-***@gromacs.org
>> Subject: Re: [gmx-users] Umbrella sampling
>>       To: gmx-***@gromacs.org
>>
>> Hi,
>>
>> There could be format problem. You can create your own .dat files by
>> typing
>> it. You have probably copied it from somewhere. I hope it will work
then.
>>
>>
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html
>>
>> Thanks
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests
>> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or send a mail to gmx-users-***@gromacs.org.
>>
>> Hii
>> I have solved the problem. It was just because of one extra space added
>> in
>> the tpr-files.dat file. Now its running properly.
>>
>> ----- End message from Dhaniram Mahato <***@gmail.com> -----
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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>> send a mail to gmx-users-***@gromacs.org.
>> --
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>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
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>> send a mail to gmx-users-***@gromacs.org.
>
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Thank you Mark for your suggestion.

----- End message from Mark Abraham <***@gmail.com> -----
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[Jefferies D.F.]

All sorted now.

Thanks,

Damien
________________________________________
From: gromacs.org_gmx-users-***@maillist.sys.kth.se [gromacs.org_gmx-users-***@maillist.sys.kth.se] on behalf of ***@iacs.res.in [***@iacs.res.in]
Sent: Friday, December 22, 2017 11:49 AM
To: gromacs.org_gmx-***@maillist.sys.kth.se
Subject: Re: [gmx-users] Umbrella sampling

----- Message from Mark Abraham <***@gmail.com> ---------
Date: Fri, 22 Dec 2017 00:42:31 +0000
From: Mark Abraham <***@gmail.com>
Reply-To: gmx-***@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
To: gmx-***@gromacs.org
Cc: gromacs.org_gmx-***@maillist.sys.kth.se

> Hi,
>
> Yes, the parsing of that file looks like it doesn't handle blank lines
> gracefully, at least. Use a text editor and clean things up. And make
sure
> the file endings are unix style, e.g. with dos2unix if relevant.
>
> Mark
>
> On Wed, Dec 20, 2017 at 7:57 AM Jefferies D.F. <***@soton.ac.uk>
> wrote:
>
>> Out of curiosity, how did you manage to identify and subsequently remove
>> the extra space? I have been having similar problems and the tools I've
>> used haven't fixed this problem.
>>
>> Thanks,
>> ________________________________________
>> From: gromacs.org_gmx-users-***@maillist.sys.kth.se [
>> gromacs.org_gmx-users-***@maillist.sys.kth.se] on behalf of
>> ***@iacs.res.in [***@iacs.res.in]
>> Sent: Tuesday, December 19, 2017 6:21 PM
>> To: gromacs.org_gmx-***@maillist.sys.kth.se
>> Subject: Re: [gmx-users] Umbrella sampling
>>
>> ----- Message from Dhaniram Mahato <***@gmail.com> ---------
>> Date: Tue, 19 Dec 2017 21:30:05 +0800
>> From: Dhaniram Mahato <***@gmail.com>
>> Reply-To: gmx-***@gromacs.org
>> Subject: Re: [gmx-users] Umbrella sampling
>> To: gmx-***@gromacs.org
>>
>> Hi,
>>
>> There could be format problem. You can create your own .dat files by
>> typing
>> it. You have probably copied it from somewhere. I hope it will work
then.
>>
>>
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html
>>
>> Thanks
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests
>> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or send a mail to gmx-users-***@gromacs.org.
>>
>> Hii
>> I have solved the problem. It was just because of one extra space added
>> in
>> the tpr-files.dat file. Now its running properly.
>>
>> ----- End message from Dhaniram Mahato <***@gmail.com> -----
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
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>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-***@gromacs.org.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
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>> send a mail to gmx-users-***@gromacs.org.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Thank you Mark for your suggestion.

----- End message from Mark Abraham <***@gmail.com> -----
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[s***@iacs.res.in]

----- Message from "Jefferies D.F." <***@soton.ac.uk> ---------
    Date: Tue, 19 Dec 2017 20:56:34 +0000
    From: "Jefferies D.F." <***@soton.ac.uk>
Reply-To: gmx-***@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
      To: gmx-***@gromacs.org,
gromacs.org_gmx-***@maillist.sys.kth.se

> Out of curiosity, how did you manage to identify and subsequently remove
> the extra space? I have been having similar problems and the tools I've
> used haven't fixed this problem.
>
> Thanks,
> ________________________________________
> From: gromacs.org_gmx-users-***@maillist.sys.kth.se
> [gromacs.org_gmx-users-***@maillist.sys.kth.se] on behalf of
> ***@iacs.res.in [***@iacs.res.in]
> Sent: Tuesday, December 19, 2017 6:21 PM
> To: gromacs.org_gmx-***@maillist.sys.kth.se
> Subject: Re: [gmx-users] Umbrella sampling
>
> ----- Message from Dhaniram Mahato <***@gmail.com> ---------
>    Date: Tue, 19 Dec 2017 21:30:05 +0800
>    From: Dhaniram Mahato <***@gmail.com>
> Reply-To: gmx-***@gromacs.org
> Subject: Re: [gmx-users] Umbrella sampling
>      To: gmx-***@gromacs.org
>
>> Hi,
>>
>> There could be format problem. You can create your own .dat files by
>> typing
>> it. You have probably copied it from somewhere. I hope it will work
then.
>>  
>
>
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html
>> Thanks
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests
>> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or send a mail to gmx-users-***@gromacs.org.
>
> Hii
> I have solved the problem. It was just because of one extra space added
in
> the tpr-files.dat file. Now its running properly.
>
> ----- End message from Dhaniram Mahato <***@gmail.com> -----
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-***@gromacs.org.
> --
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>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests
> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or send a mail to gmx-users-***@gromacs.org.

Hii
In my tpr-files.dat file as I showed in the first mail, one extra blank
line was added at the bottom of the file. I just deleted that line and the
problem has been solved. You just open your .dat file and do shift+g then
see if there is a extra line or not.
Sunipa

----- End message from "Jefferies D.F." <***@soton.ac.uk> -----
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