Discussion:
[gmx-users] Queries regarding temperature gradient
Sabreen Farnaz
2018-07-05 19:56:25 UTC
Permalink
Dear all,

I am setting up a system where I want the solute to be immersed in a
solvent with a temperature gradient. I have defined two different
temperature groups, two portions of the solvent, and want them to be at say
T1 and T2 kelvins. The rest of the system will not be subjected to a
thermostat (tau_t=-1).
My questions are:
1. Should NVT and NPT mdp files also have the same t_ref and tau_t? A
tau_t=-1 gives a warning in nvt grompp, can it be ignored?
2. I am generating velocities in nvt run and continuing npt with previous
velocities. For production run, I only take the equilibrated structure and
generate velocities again. (No continuation)
Should gen_temp have the same temperature values in each of nvt and md mdp
files?

Please help.
Thank you!

Regards,
Neelima S.
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Sabreen Farnaz
2018-07-06 17:07:10 UTC
Permalink
Dear all,
This is in regard to my previous queries. The warning in NVT step can
possibly be ignored using -maxwarn but I am still not sure about the rest!
Can someone please help?

Thanks,
Neelima S.
Post by Sabreen Farnaz
Dear all,
I am setting up a system where I want the solute to be immersed in a
solvent with a temperature gradient. I have defined two different
temperature groups, two portions of the solvent, and want them to be at say
T1 and T2 kelvins. The rest of the system will not be subjected to a
thermostat (tau_t=-1).
1. Should NVT and NPT mdp files also have the same t_ref and tau_t? A
tau_t=-1 gives a warning in nvt grompp, can it be ignored?
2. I am generating velocities in nvt run and continuing npt with previous
velocities. For production run, I only take the equilibrated structure and
generate velocities again. (No continuation)
Should gen_temp have the same temperature values in each of nvt and md mdp
files?
Please help.
Thank you!
Regards,
Neelima S.
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Justin Lemkul
2018-07-06 18:00:38 UTC
Permalink
Post by Sabreen Farnaz
Dear all,
This is in regard to my previous queries. The warning in NVT step can
possibly be ignored using -maxwarn but I am still not sure about the rest!
Can someone please help?
tau_t = -1 means temperature coupling is not applied. Whether that's
what you want or not is up to you, but in that case, your ensembles are
not NVT or NPT, because T is no longer conserved.
Post by Sabreen Farnaz
Thanks,
Neelima S.
Post by Sabreen Farnaz
Dear all,
I am setting up a system where I want the solute to be immersed in a
solvent with a temperature gradient. I have defined two different
temperature groups, two portions of the solvent, and want them to be at say
T1 and T2 kelvins. The rest of the system will not be subjected to a
thermostat (tau_t=-1).
Realize that with PBC, you're not likely to get what you want. I don't
know how you're defining the T1 and T2 groups, but if they're in contact
via PBC, the "gradient" really doesn't exist - you have a hot and cold
bath directly in contact. See previous threads on temperature gradients
for more discussion. If the T1 and T2 groups are capable of diffusing,
then you definitely don't have a gradient.
Post by Sabreen Farnaz
Post by Sabreen Farnaz
1. Should NVT and NPT mdp files also have the same t_ref and tau_t? A
tau_t=-1 gives a warning in nvt grompp, can it be ignored?
2. I am generating velocities in nvt run and continuing npt with previous
velocities. For production run, I only take the equilibrated structure and
generate velocities again. (No continuation)
If you're re-generating velocities, what was the point of the previous
equilibration steps? You're just re-setting your system to a random state.
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Should gen_temp have the same temperature values in each of nvt and md mdp
files?
If you intend to model the same ensemble, yes, but again re-generating
velocities after equilibrating doesn't make much sense to me.

-Justin
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Please help.
Thank you!
Regards,
Neelima S.
--
==================================================

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

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

***@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================
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Sabreen Farnaz
2018-07-06 20:30:38 UTC
Permalink
Dear Dr. Lemkul,
Thank you for your answer. Can you please also advise how can I get the
temperature of a system as a function of distance using gromacs 5.1.5? gmx
energy plots the temperature of the centre of mass of energy groups against
time. gmx traj also does the same from velocity information.

Regards,
Neelima S.
Post by Justin Lemkul
Post by Sabreen Farnaz
Dear all,
This is in regard to my previous queries. The warning in NVT step can
possibly be ignored using -maxwarn but I am still not sure about the
rest!
Post by Sabreen Farnaz
Can someone please help?
tau_t = -1 means temperature coupling is not applied. Whether that's
what you want or not is up to you, but in that case, your ensembles are
not NVT or NPT, because T is no longer conserved.
Post by Sabreen Farnaz
Thanks,
Neelima S.
Post by Sabreen Farnaz
Dear all,
I am setting up a system where I want the solute to be immersed in a
solvent with a temperature gradient. I have defined two different
temperature groups, two portions of the solvent, and want them to be at
say
Post by Sabreen Farnaz
Post by Sabreen Farnaz
T1 and T2 kelvins. The rest of the system will not be subjected to a
thermostat (tau_t=-1).
Realize that with PBC, you're not likely to get what you want. I don't
know how you're defining the T1 and T2 groups, but if they're in contact
via PBC, the "gradient" really doesn't exist - you have a hot and cold
bath directly in contact. See previous threads on temperature gradients
for more discussion. If the T1 and T2 groups are capable of diffusing,
then you definitely don't have a gradient.
Post by Sabreen Farnaz
Post by Sabreen Farnaz
1. Should NVT and NPT mdp files also have the same t_ref and tau_t? A
tau_t=-1 gives a warning in nvt grompp, can it be ignored?
2. I am generating velocities in nvt run and continuing npt with
previous
Post by Sabreen Farnaz
Post by Sabreen Farnaz
velocities. For production run, I only take the equilibrated structure
and
Post by Sabreen Farnaz
Post by Sabreen Farnaz
generate velocities again. (No continuation)
If you're re-generating velocities, what was the point of the previous
equilibration steps? You're just re-setting your system to a random state.
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Should gen_temp have the same temperature values in each of nvt and md
mdp
Post by Sabreen Farnaz
Post by Sabreen Farnaz
files?
If you intend to model the same ensemble, yes, but again re-generating
velocities after equilibrating doesn't make much sense to me.
-Justin
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Please help.
Thank you!
Regards,
Neelima S.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
http://www.thelemkullab.com
==================================================
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Justin Lemkul
2018-07-08 18:09:42 UTC
Permalink
Post by Sabreen Farnaz
Dear Dr. Lemkul,
Thank you for your answer. Can you please also advise how can I get the
temperature of a system as a function of distance using gromacs 5.1.5? gmx
energy plots the temperature of the centre of mass of energy groups against
time. gmx traj also does the same from velocity information.
If it can even be done, it will be very time-consuming. You'd have to
run gmx select on each frame of the trajectory to specify a selection of
atoms that falls within some region of space. With that index group,
you'd have to use gmx traj to extract the velocities of that selection
in that frame, then compute the temperature. Then repeat that for every
slice in every frame, each individually, since most tools do not yet
support dynamic selections.

-Justin
Post by Sabreen Farnaz
Regards,
Neelima S.
Post by Justin Lemkul
Post by Sabreen Farnaz
Dear all,
This is in regard to my previous queries. The warning in NVT step can
possibly be ignored using -maxwarn but I am still not sure about the
rest!
Post by Sabreen Farnaz
Can someone please help?
tau_t = -1 means temperature coupling is not applied. Whether that's
what you want or not is up to you, but in that case, your ensembles are
not NVT or NPT, because T is no longer conserved.
Post by Sabreen Farnaz
Thanks,
Neelima S.
Post by Sabreen Farnaz
Dear all,
I am setting up a system where I want the solute to be immersed in a
solvent with a temperature gradient. I have defined two different
temperature groups, two portions of the solvent, and want them to be at
say
Post by Sabreen Farnaz
Post by Sabreen Farnaz
T1 and T2 kelvins. The rest of the system will not be subjected to a
thermostat (tau_t=-1).
Realize that with PBC, you're not likely to get what you want. I don't
know how you're defining the T1 and T2 groups, but if they're in contact
via PBC, the "gradient" really doesn't exist - you have a hot and cold
bath directly in contact. See previous threads on temperature gradients
for more discussion. If the T1 and T2 groups are capable of diffusing,
then you definitely don't have a gradient.
Post by Sabreen Farnaz
Post by Sabreen Farnaz
1. Should NVT and NPT mdp files also have the same t_ref and tau_t? A
tau_t=-1 gives a warning in nvt grompp, can it be ignored?
2. I am generating velocities in nvt run and continuing npt with
previous
Post by Sabreen Farnaz
Post by Sabreen Farnaz
velocities. For production run, I only take the equilibrated structure
and
Post by Sabreen Farnaz
Post by Sabreen Farnaz
generate velocities again. (No continuation)
If you're re-generating velocities, what was the point of the previous
equilibration steps? You're just re-setting your system to a random state.
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Should gen_temp have the same temperature values in each of nvt and md
mdp
Post by Sabreen Farnaz
Post by Sabreen Farnaz
files?
If you intend to model the same ensemble, yes, but again re-generating
velocities after equilibrating doesn't make much sense to me.
-Justin
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Please help.
Thank you!
Regards,
Neelima S.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
http://www.thelemkullab.com
==================================================
--
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
--
==================================================

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

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

***@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================
--
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Sabreen Farnaz
2018-07-08 18:21:41 UTC
Permalink
Thank you, Dr. Lemkul. I have done this but used gmx energy to find the
temperature of each frame (defined as separate energy groups) in place of
gmx traj.
Can you please elaborate what is the difference between the temperature
calculated by these two commands? (gmx energy and gmx traj) I have found
different values for the same energy group using them.
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Dear Dr. Lemkul,
Thank you for your answer. Can you please also advise how can I get the
temperature of a system as a function of distance using gromacs 5.1.5?
gmx
Post by Sabreen Farnaz
energy plots the temperature of the centre of mass of energy groups
against
Post by Sabreen Farnaz
time. gmx traj also does the same from velocity information.
If it can even be done, it will be very time-consuming. You'd have to
run gmx select on each frame of the trajectory to specify a selection of
atoms that falls within some region of space. With that index group,
you'd have to use gmx traj to extract the velocities of that selection
in that frame, then compute the temperature. Then repeat that for every
slice in every frame, each individually, since most tools do not yet
support dynamic selections.
-Justin
Post by Sabreen Farnaz
Regards,
Neelima S.
Post by Justin Lemkul
Post by Sabreen Farnaz
Dear all,
This is in regard to my previous queries. The warning in NVT step can
possibly be ignored using -maxwarn but I am still not sure about the
rest!
Post by Sabreen Farnaz
Can someone please help?
tau_t = -1 means temperature coupling is not applied. Whether that's
what you want or not is up to you, but in that case, your ensembles are
not NVT or NPT, because T is no longer conserved.
Post by Sabreen Farnaz
Thanks,
Neelima S.
Post by Sabreen Farnaz
Dear all,
I am setting up a system where I want the solute to be immersed in a
solvent with a temperature gradient. I have defined two different
temperature groups, two portions of the solvent, and want them to be
at
Post by Sabreen Farnaz
Post by Justin Lemkul
say
Post by Sabreen Farnaz
Post by Sabreen Farnaz
T1 and T2 kelvins. The rest of the system will not be subjected to a
thermostat (tau_t=-1).
Realize that with PBC, you're not likely to get what you want. I don't
know how you're defining the T1 and T2 groups, but if they're in contact
via PBC, the "gradient" really doesn't exist - you have a hot and cold
bath directly in contact. See previous threads on temperature gradients
for more discussion. If the T1 and T2 groups are capable of diffusing,
then you definitely don't have a gradient.
Post by Sabreen Farnaz
Post by Sabreen Farnaz
1. Should NVT and NPT mdp files also have the same t_ref and tau_t? A
tau_t=-1 gives a warning in nvt grompp, can it be ignored?
2. I am generating velocities in nvt run and continuing npt with
previous
Post by Sabreen Farnaz
Post by Sabreen Farnaz
velocities. For production run, I only take the equilibrated structure
and
Post by Sabreen Farnaz
Post by Sabreen Farnaz
generate velocities again. (No continuation)
If you're re-generating velocities, what was the point of the previous
equilibration steps? You're just re-setting your system to a random
state.
Post by Sabreen Farnaz
Post by Justin Lemkul
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Should gen_temp have the same temperature values in each of nvt and md
mdp
Post by Sabreen Farnaz
Post by Sabreen Farnaz
files?
If you intend to model the same ensemble, yes, but again re-generating
velocities after equilibrating doesn't make much sense to me.
-Justin
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Please help.
Thank you!
Regards,
Neelima S.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
http://www.thelemkullab.com
==================================================
--
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
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
http://www.thelemkullab.com
==================================================
--
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* Please search the archive at
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Mark Abraham
2018-07-08 18:25:53 UTC
Permalink
Hi,

gmx help traj has a useful point to make about how it estimates temperature
from the velocities.

Mark
Post by Sabreen Farnaz
Thank you, Dr. Lemkul. I have done this but used gmx energy to find the
temperature of each frame (defined as separate energy groups) in place of
gmx traj.
Can you please elaborate what is the difference between the temperature
calculated by these two commands? (gmx energy and gmx traj) I have found
different values for the same energy group using them.
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Dear Dr. Lemkul,
Thank you for your answer. Can you please also advise how can I get the
temperature of a system as a function of distance using gromacs 5.1.5?
gmx
Post by Sabreen Farnaz
energy plots the temperature of the centre of mass of energy groups
against
Post by Sabreen Farnaz
time. gmx traj also does the same from velocity information.
If it can even be done, it will be very time-consuming. You'd have to
run gmx select on each frame of the trajectory to specify a selection of
atoms that falls within some region of space. With that index group,
you'd have to use gmx traj to extract the velocities of that selection
in that frame, then compute the temperature. Then repeat that for every
slice in every frame, each individually, since most tools do not yet
support dynamic selections.
-Justin
Post by Sabreen Farnaz
Regards,
Neelima S.
Post by Justin Lemkul
Post by Sabreen Farnaz
Dear all,
This is in regard to my previous queries. The warning in NVT step can
possibly be ignored using -maxwarn but I am still not sure about the
rest!
Post by Sabreen Farnaz
Can someone please help?
tau_t = -1 means temperature coupling is not applied. Whether that's
what you want or not is up to you, but in that case, your ensembles
are
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
not NVT or NPT, because T is no longer conserved.
Post by Sabreen Farnaz
Thanks,
Neelima S.
Post by Sabreen Farnaz
Dear all,
I am setting up a system where I want the solute to be immersed in a
solvent with a temperature gradient. I have defined two different
temperature groups, two portions of the solvent, and want them to be
at
Post by Sabreen Farnaz
Post by Justin Lemkul
say
Post by Sabreen Farnaz
Post by Sabreen Farnaz
T1 and T2 kelvins. The rest of the system will not be subjected to a
thermostat (tau_t=-1).
Realize that with PBC, you're not likely to get what you want. I don't
know how you're defining the T1 and T2 groups, but if they're in
contact
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
via PBC, the "gradient" really doesn't exist - you have a hot and cold
bath directly in contact. See previous threads on temperature
gradients
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
for more discussion. If the T1 and T2 groups are capable of diffusing,
then you definitely don't have a gradient.
Post by Sabreen Farnaz
Post by Sabreen Farnaz
1. Should NVT and NPT mdp files also have the same t_ref and tau_t?
A
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
Post by Sabreen Farnaz
Post by Sabreen Farnaz
tau_t=-1 gives a warning in nvt grompp, can it be ignored?
2. I am generating velocities in nvt run and continuing npt with
previous
Post by Sabreen Farnaz
Post by Sabreen Farnaz
velocities. For production run, I only take the equilibrated
structure
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
and
Post by Sabreen Farnaz
Post by Sabreen Farnaz
generate velocities again. (No continuation)
If you're re-generating velocities, what was the point of the previous
equilibration steps? You're just re-setting your system to a random
state.
Post by Sabreen Farnaz
Post by Justin Lemkul
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Should gen_temp have the same temperature values in each of nvt and
md
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
mdp
Post by Sabreen Farnaz
Post by Sabreen Farnaz
files?
If you intend to model the same ensemble, yes, but again re-generating
velocities after equilibrating does
<https://maps.google.com/?q=%0A%3E+%3E%3E+velocities+after+equilibrating+does&entry=gmail&source=g>n't
make much sense to me.
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
-Justin
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Please help.
Thank you!
Regards,
Neelima S.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
http://www.thelemkullab.com
==================================================
--
Gromacs Users mailing list
* Please search the archive at
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* For (un)subscribe requests visit
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--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
http://www.thelemkullab.com
==================================================
--
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Sabreen Farnaz
2018-07-08 18:37:47 UTC
Permalink
I had read this part from gmx help traj "plots temperature of each group,
provides velocities are present...no corrections are made for constraines
degrees of freedom..."

Looks like it uses Kinetic energy from velocity to calculate the
temperature. My question is, is it supposed to be different than that
calculated by gmx energy? It is to be noted that in my case the temperature
calculated by gmx energy after production run is same as that specified in
nvt/npt steps. But temp from gmx traj is much less.

Thanks a lot for your help.
Post by Mark Abraham
Hi,
gmx help traj has a useful point to make about how it estimates temperature
from the velocities.
Mark
Post by Sabreen Farnaz
Thank you, Dr. Lemkul. I have done this but used gmx energy to find the
temperature of each frame (defined as separate energy groups) in place of
gmx traj.
Can you please elaborate what is the difference between the temperature
calculated by these two commands? (gmx energy and gmx traj) I have found
different values for the same energy group using them.
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Dear Dr. Lemkul,
Thank you for your answer. Can you please also advise how can I get
the
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
temperature of a system as a function of distance using gromacs
5.1.5?
Post by Sabreen Farnaz
Post by Sabreen Farnaz
gmx
Post by Sabreen Farnaz
energy plots the temperature of the centre of mass of energy groups
against
Post by Sabreen Farnaz
time. gmx traj also does the same from velocity information.
If it can even be done, it will be very time-consuming. You'd have to
run gmx select on each frame of the trajectory to specify a selection
of
Post by Sabreen Farnaz
Post by Sabreen Farnaz
atoms that falls within some region of space. With that index group,
you'd have to use gmx traj to extract the velocities of that selection
in that frame, then compute the temperature. Then repeat that for every
slice in every frame, each individually, since most tools do not yet
support dynamic selections.
-Justin
Post by Sabreen Farnaz
Regards,
Neelima S.
Post by Justin Lemkul
Post by Sabreen Farnaz
Dear all,
This is in regard to my previous queries. The warning in NVT step
can
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
Post by Sabreen Farnaz
possibly be ignored using -maxwarn but I am still not sure about
the
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
rest!
Post by Sabreen Farnaz
Can someone please help?
tau_t = -1 means temperature coupling is not applied. Whether that's
what you want or not is up to you, but in that case, your ensembles
are
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
not NVT or NPT, because T is no longer conserved.
Post by Sabreen Farnaz
Thanks,
Neelima S.
Post by Sabreen Farnaz
Dear all,
I am setting up a system where I want the solute to be immersed
in a
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
Post by Sabreen Farnaz
Post by Sabreen Farnaz
solvent with a temperature gradient. I have defined two different
temperature groups, two portions of the solvent, and want them to
be
Post by Sabreen Farnaz
Post by Sabreen Farnaz
at
Post by Sabreen Farnaz
Post by Justin Lemkul
say
Post by Sabreen Farnaz
Post by Sabreen Farnaz
T1 and T2 kelvins. The rest of the system will not be subjected
to a
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
Post by Sabreen Farnaz
Post by Sabreen Farnaz
thermostat (tau_t=-1).
Realize that with PBC, you're not likely to get what you want. I
don't
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
know how you're defining the T1 and T2 groups, but if they're in
contact
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
via PBC, the "gradient" really doesn't exist - you have a hot and
cold
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
bath directly in contact. See previous threads on temperature
gradients
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
for more discussion. If the T1 and T2 groups are capable of
diffusing,
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
then you definitely don't have a gradient.
Post by Sabreen Farnaz
Post by Sabreen Farnaz
1. Should NVT and NPT mdp files also have the same t_ref and
tau_t?
Post by Sabreen Farnaz
A
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
Post by Sabreen Farnaz
Post by Sabreen Farnaz
tau_t=-1 gives a warning in nvt grompp, can it be ignored?
2. I am generating velocities in nvt run and continuing npt with
previous
Post by Sabreen Farnaz
Post by Sabreen Farnaz
velocities. For production run, I only take the equilibrated
structure
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
and
Post by Sabreen Farnaz
Post by Sabreen Farnaz
generate velocities again. (No continuation)
If you're re-generating velocities, what was the point of the
previous
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
equilibration steps? You're just re-setting your system to a random
state.
Post by Sabreen Farnaz
Post by Justin Lemkul
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Should gen_temp have the same temperature values in each of nvt
and
Post by Sabreen Farnaz
md
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
mdp
Post by Sabreen Farnaz
Post by Sabreen Farnaz
files?
If you intend to model the same ensemble, yes, but again
re-generating
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
velocities after equilibrating does
<
https://maps.google.com/?q=%0A%3E+%3E%3E+velocities+after+equilibrating+does&entry=gmail&source=g
Post by Sabreen Farnaz
n't
make much sense to me.
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
-Justin
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Please help.
Thank you!
Regards,
Neelima S.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
http://www.thelemkullab.com
==================================================
--
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* For (un)subscribe requests visit
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or
Post by Sabreen Farnaz
Post by Sabreen Farnaz
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
http://www.thelemkullab.com
==================================================
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Justin Lemkul
2018-07-08 18:39:35 UTC
Permalink
Post by Sabreen Farnaz
I had read this part from gmx help traj "plots temperature of each group,
provides velocities are present...no corrections are made for constraines
degrees of freedom..."
And therein lies the difference. gmx energy has the correct number of
degrees of freedom, gmx traj has no knowledge of such information,
meaning you have to perform a correction on its resulting temperature.

-Justin
Post by Sabreen Farnaz
Looks like it uses Kinetic energy from velocity to calculate the
temperature. My question is, is it supposed to be different than that
calculated by gmx energy? It is to be noted that in my case the temperature
calculated by gmx energy after production run is same as that specified in
nvt/npt steps. But temp from gmx traj is much less.
Thanks a lot for your help.
Post by Mark Abraham
Hi,
gmx help traj has a useful point to make about how it estimates temperature
from the velocities.
Mark
Post by Sabreen Farnaz
Thank you, Dr. Lemkul. I have done this but used gmx energy to find the
temperature of each frame (defined as separate energy groups) in place of
gmx traj.
Can you please elaborate what is the difference between the temperature
calculated by these two commands? (gmx energy and gmx traj) I have found
different values for the same energy group using them.
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Dear Dr. Lemkul,
Thank you for your answer. Can you please also advise how can I get
the
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
temperature of a system as a function of distance using gromacs
5.1.5?
Post by Sabreen Farnaz
Post by Sabreen Farnaz
gmx
Post by Sabreen Farnaz
energy plots the temperature of the centre of mass of energy groups
against
Post by Sabreen Farnaz
time. gmx traj also does the same from velocity information.
If it can even be done, it will be very time-consuming. You'd have to
run gmx select on each frame of the trajectory to specify a selection
of
Post by Sabreen Farnaz
Post by Sabreen Farnaz
atoms that falls within some region of space. With that index group,
you'd have to use gmx traj to extract the velocities of that selection
in that frame, then compute the temperature. Then repeat that for every
slice in every frame, each individually, since most tools do not yet
support dynamic selections.
-Justin
Post by Sabreen Farnaz
Regards,
Neelima S.
Post by Justin Lemkul
Post by Sabreen Farnaz
Dear all,
This is in regard to my previous queries. The warning in NVT step
can
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
Post by Sabreen Farnaz
possibly be ignored using -maxwarn but I am still not sure about
the
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
rest!
Post by Sabreen Farnaz
Can someone please help?
tau_t = -1 means temperature coupling is not applied. Whether that's
what you want or not is up to you, but in that case, your ensembles
are
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
not NVT or NPT, because T is no longer conserved.
Post by Sabreen Farnaz
Thanks,
Neelima S.
Post by Sabreen Farnaz
Dear all,
I am setting up a system where I want the solute to be immersed
in a
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
Post by Sabreen Farnaz
Post by Sabreen Farnaz
solvent with a temperature gradient. I have defined two different
temperature groups, two portions of the solvent, and want them to
be
Post by Sabreen Farnaz
Post by Sabreen Farnaz
at
Post by Sabreen Farnaz
Post by Justin Lemkul
say
Post by Sabreen Farnaz
Post by Sabreen Farnaz
T1 and T2 kelvins. The rest of the system will not be subjected
to a
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
Post by Sabreen Farnaz
Post by Sabreen Farnaz
thermostat (tau_t=-1).
Realize that with PBC, you're not likely to get what you want. I
don't
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
know how you're defining the T1 and T2 groups, but if they're in
contact
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
via PBC, the "gradient" really doesn't exist - you have a hot and
cold
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
bath directly in contact. See previous threads on temperature
gradients
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
for more discussion. If the T1 and T2 groups are capable of
diffusing,
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
then you definitely don't have a gradient.
Post by Sabreen Farnaz
Post by Sabreen Farnaz
1. Should NVT and NPT mdp files also have the same t_ref and
tau_t?
Post by Sabreen Farnaz
A
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
Post by Sabreen Farnaz
Post by Sabreen Farnaz
tau_t=-1 gives a warning in nvt grompp, can it be ignored?
2. I am generating velocities in nvt run and continuing npt with
previous
Post by Sabreen Farnaz
Post by Sabreen Farnaz
velocities. For production run, I only take the equilibrated
structure
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
and
Post by Sabreen Farnaz
Post by Sabreen Farnaz
generate velocities again. (No continuation)
If you're re-generating velocities, what was the point of the
previous
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
equilibration steps? You're just re-setting your system to a random
state.
Post by Sabreen Farnaz
Post by Justin Lemkul
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Should gen_temp have the same temperature values in each of nvt
and
Post by Sabreen Farnaz
md
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
mdp
Post by Sabreen Farnaz
Post by Sabreen Farnaz
files?
If you intend to model the same ensemble, yes, but again
re-generating
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
velocities after equilibrating does
<
https://maps.google.com/?q=%0A%3E+%3E%3E+velocities+after+equilibrating+does&entry=gmail&source=g
Post by Sabreen Farnaz
n't
make much sense to me.
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
-Justin
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Please help.
Thank you!
Regards,
Neelima S.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
http://www.thelemkullab.com
==================================================
--
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
Post by Sabreen Farnaz
Post by Sabreen Farnaz
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
http://www.thelemkullab.com
==================================================
--
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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* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
--
==================================================

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

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

***@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================
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Sabreen Farnaz
2018-07-08 18:48:48 UTC
Permalink
That makes sense.
Thanks a lot, lot for your help.
Post by Justin Lemkul
Post by Sabreen Farnaz
I had read this part from gmx help traj "plots temperature of each group,
provides velocities are present...no corrections are made for constraines
degrees of freedom..."
And therein lies the difference. gmx energy has the correct number of
degrees of freedom, gmx traj has no knowledge of such information,
meaning you have to perform a correction on its resulting temperature.
-Justin
Post by Sabreen Farnaz
Looks like it uses Kinetic energy from velocity to calculate the
temperature. My question is, is it supposed to be different than that
calculated by gmx energy? It is to be noted that in my case the
temperature
Post by Sabreen Farnaz
calculated by gmx energy after production run is same as that specified
in
Post by Sabreen Farnaz
nvt/npt steps. But temp from gmx traj is much less.
Thanks a lot for your help.
Post by Mark Abraham
Hi,
gmx help traj has a useful point to make about how it estimates
temperature
Post by Sabreen Farnaz
Post by Mark Abraham
from the velocities.
Mark
Post by Sabreen Farnaz
Thank you, Dr. Lemkul. I have done this but used gmx energy to find the
temperature of each frame (defined as separate energy groups) in place
of
Post by Sabreen Farnaz
Post by Mark Abraham
Post by Sabreen Farnaz
gmx traj.
Can you please elaborate what is the difference between the temperature
calculated by these two commands? (gmx energy and gmx traj) I have
found
Post by Sabreen Farnaz
Post by Mark Abraham
Post by Sabreen Farnaz
different values for the same energy group using them.
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Dear Dr. Lemkul,
Thank you for your answer. Can you please also advise how can I get
the
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
temperature of a system as a function of distance using gromacs
5.1.5?
Post by Sabreen Farnaz
Post by Sabreen Farnaz
gmx
Post by Sabreen Farnaz
energy plots the temperature of the centre of mass of energy groups
against
Post by Sabreen Farnaz
time. gmx traj also does the same from velocity information.
If it can even be done, it will be very time-consuming. You'd have to
run gmx select on each frame of the trajectory to specify a selection
of
Post by Sabreen Farnaz
Post by Sabreen Farnaz
atoms that falls within some region of space. With that index group,
you'd have to use gmx traj to extract the velocities of that selection
in that frame, then compute the temperature. Then repeat that for
every
Post by Sabreen Farnaz
Post by Mark Abraham
Post by Sabreen Farnaz
Post by Sabreen Farnaz
slice in every frame, each individually, since most tools do not yet
support dynamic selections.
-Justin
Post by Sabreen Farnaz
Regards,
Neelima S.
Post by Justin Lemkul
Post by Sabreen Farnaz
Dear all,
This is in regard to my previous queries. The warning in NVT step
can
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
Post by Sabreen Farnaz
possibly be ignored using -maxwarn but I am still not sure about
the
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
rest!
Post by Sabreen Farnaz
Can someone please help?
tau_t = -1 means temperature coupling is not applied. Whether that's
what you want or not is up to you, but in that case, your ensembles
are
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
not NVT or NPT, because T is no longer conserved.
Post by Sabreen Farnaz
Thanks,
Neelima S.
Post by Sabreen Farnaz
Dear all,
I am setting up a system where I want the solute to be immersed
in a
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
Post by Sabreen Farnaz
Post by Sabreen Farnaz
solvent with a temperature gradient. I have defined two different
temperature groups, two portions of the solvent, and want them to
be
Post by Sabreen Farnaz
Post by Sabreen Farnaz
at
Post by Sabreen Farnaz
Post by Justin Lemkul
say
Post by Sabreen Farnaz
Post by Sabreen Farnaz
T1 and T2 kelvins. The rest of the system will not be subjected
to a
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
Post by Sabreen Farnaz
Post by Sabreen Farnaz
thermostat (tau_t=-1).
Realize that with PBC, you're not likely to get what you want. I
don't
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
know how you're defining the T1 and T2 groups, but if they're in
contact
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
via PBC, the "gradient" really doesn't exist - you have a hot and
cold
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
bath directly in contact. See previous threads on temperature
gradients
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
for more discussion. If the T1 and T2 groups are capable of
diffusing,
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
then you definitely don't have a gradient.
Post by Sabreen Farnaz
Post by Sabreen Farnaz
1. Should NVT and NPT mdp files also have the same t_ref and
tau_t?
Post by Sabreen Farnaz
A
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
Post by Sabreen Farnaz
Post by Sabreen Farnaz
tau_t=-1 gives a warning in nvt grompp, can it be ignored?
2. I am generating velocities in nvt run and continuing npt with
previous
Post by Sabreen Farnaz
Post by Sabreen Farnaz
velocities. For production run, I only take the equilibrated
structure
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
and
Post by Sabreen Farnaz
Post by Sabreen Farnaz
generate velocities again. (No continuation)
If you're re-generating velocities, what was the point of the
previous
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
equilibration steps? You're just re-setting your system to a random
state.
Post by Sabreen Farnaz
Post by Justin Lemkul
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Should gen_temp have the same temperature values in each of nvt
and
Post by Sabreen Farnaz
md
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
mdp
Post by Sabreen Farnaz
Post by Sabreen Farnaz
files?
If you intend to model the same ensemble, yes, but again
re-generating
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
velocities after equilibrating does
<
https://maps.google.com/?q=%0A%3E+%3E%3E+velocities+after+equilibrating+does&entry=gmail&source=g
Post by Sabreen Farnaz
Post by Mark Abraham
Post by Sabreen Farnaz
n't
make much sense to me.
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Post by Justin Lemkul
-Justin
Post by Sabreen Farnaz
Post by Sabreen Farnaz
Please help.
Thank you!
Regards,
Neelima S.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
http://www.thelemkullab.com
==================================================
--
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
Post by Sabreen Farnaz
Post by Sabreen Farnaz
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
http://www.thelemkullab.com
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
http://www.thelemkullab.com
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