[gmx-users] gromacs.org_gmx-users Digest, Vol 176, Issue 11

Seketoulie Keretsu

2018-12-07 06:12:12 UTC

Dear
Thank you.

"yum install numpy" worked for me. Surprised why i haven't tried that long back.
On Fri, Dec 7, 2018 at 1:41 PM

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1. Re: numpy related problem in GROMACS protein-ligand file
preperation (Benson Muite)
2. How restrain the end-to-end distance in simulation?
(Mehdi Bagherpour)
3. Re: mdrun-adjusted cutoffs?! (Alex)
4. Re: mdrun-adjusted cutoffs?! (Mark Abraham)
----------------------------------------------------------------------
Message: 1
Date: Thu, 6 Dec 2018 12:51:35 +0000
Subject: Re: [gmx-users] numpy related problem in GROMACS
protein-ligand file preperation
Content-Type: text/plain; charset="utf-8"
Hi Seketoulie,
If you have administrator rights on a CentOS system
sudo yum search numpy
will let you know what numpy versions have already been packaged.
You can also use
pip install --user numpy
https://docs.scipy.org/doc/numpy-1.10.1/user/install.html
Regards,
Benson

Dear Experts,
I am fairly new to gromacs (and linux CENTOS). I have recently
installed the Gromacs18 successfully. However while doing the
Protein-Lig tutorial I came across this problem while running the
File "cgenff_charmm2gmx.py", line 46, in <module>
import numpy as np
ImportError: No module named numpy
I have python 2.7.5 installed on my system. I am unable to find
solutions related to this. Kindly advise how to correct this? A hint
on the possible cause will be awesome too.
Note: I also have Amber18 installed on my the same system which
apparently installs numpy.
Thanking you.
Sincerely,
Seketoulie

------------------------------
Message: 2
Date: Thu, 6 Dec 2018 15:58:04 +0100
Subject: [gmx-users] How restrain the end-to-end distance in
simulation?
Content-Type: text/plain; charset="UTF-8"
Dear all,
I am new in Gromacs and would like to restrain the the end-to-end distance
of a bend DNA. I mean I want to restraint the distance between COM of end
base-pairs in simulation.
I would appreciate if you could let me know how to do that.
Cheer,
Mahdi
------------------------------
Message: 3
Date: Thu, 6 Dec 2018 12:39:03 -0700
Subject: Re: [gmx-users] mdrun-adjusted cutoffs?!
Content-Type: text/plain; charset=utf-8; format=flowed
I'm not ignoring the long-range contribution, but yes, most of the
effects I am talking about are short-range. What I am asking is how much
the free energy of ionic hydration for K+ changes in, say, a system that
contains KCl in bulk water -- with and without autotuning. Hence also
the earlier question about being able to turn it off at least temporarily.
Alex

Hi,
It sounds like you are only looking at the short-ranged component of the
electrostatic interaction, and thus ignoring the way the long range
component also changes. Is the validity of the PME auto tuning the question
at hand?
Mark

More specifically, electrostatics. For the stuff I'm talking about, the
LJ portion contributes ~20% at the most. When the change in energetics
is a statistically persistent value of order kT (of which about 20%
comes from LJ), the quantity of interest (~exp(E/kT)) changes by a
factor of 2.72. Again, this is a fairly special case, but I can easily
envision someone doing ion permeation across KcsA and the currents would
be similarly affected. For instance, when I set all cutoffs at 1.0 nm,
mdrun ends up using something like 1.1 nm for electrostatics, at least
that's what I see at the top of the log.
I agree with what you said about vdW and it can be totally arbitraty and
then often requires crutches elsewhere, but my question was whether for
very sensitive quantities mdrun ends up utilizing the forcefield as it
was designed and not in a "slightly off" regime. Basically, you asked me
to describe our case and why I think there may be a slight issue, so
there it is.
Alex

Hi,
One needs to be more specific than NB. There is evidence that VDW cutoffs
of traditional lengths cause approximation errors that cause compensating
parameterization errors elsewhere; those effects get worse if the system

inhomogeneous. Accordingly, mdrun never touches VDW cutoffs.

Electrostatic

with PME is quite another matter - there you need sufficient overall
accuracy, and there are multiple equivalent ways to do that.
Mark

Hi Mark,
I am not sure it is a concern, to be honest, so let me just lay out my
thoughts and maybe you could share your opinion.
I recently shared a link for our recent paper
(https://www.nature.com/articles/s41563-018-0220-4), in which the
quantity of interest is ion current via pores that disallow what we
normally mean by diffusive permeation. Instead, there are considerable
barriers and ionic currents are rather precisely described by
exp(-E/kT), where E is some energy calculated from nonbonded
interactions and includes a huge contribution from the solvent. It is my
understanding that NB stuff gets parameterized at a particular cutoff
value and our results are rather sensitive to that. I can't say we're
dying to have extreme repeatability, but is it in your opinion
acceptable to have variability in the cutoff radii and the rlist between
something like 1.0 - 1.2 nm? To begin with, I am not particularly
worried about it, because we mostly report on qualitative behaviors, but
I am interested in your opinion. I have read the manual and
unfortunately there is nothing in the way of actually showing estimates
of NB energy variation as a function of small differences in cutoffs.
Thank you,
Alex

Hi,
There's quite detailed discussion of the treatment of pair searching in
section 3.4.2 of the reference manual. Perhaps that clarifies things?

We're

not aware of a reason to want to control things manually, but if you

have

one, we're keen to hear of it!
Mark

Hi all,
We've long noticed that at the beginning of simulations mdrun goes

through

what seems like trying to adjust the short-range NB radii to its

liking.

What is up with that and does this mean that every simulation proceeds

with

a new cutoff? If so, is there a way to disable this?
Thank you,
Alex
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------------------------------
Message: 4
Date: Fri, 7 Dec 2018 15:38:55 +1100
Subject: Re: [gmx-users] mdrun-adjusted cutoffs?!
Content-Type: text/plain; charset="UTF-8"
Hi,
Zero, because we are shifting between equivalent ways to compute the total
electrostatic interaction.
You can turn off the PME tuning with mdrun -notunepme, but unless there's a
bug, all that will do is force it to run slower than optimal. Obviously you
could try it and see that the FE of hydration does not change with the
model, so long as you have a reproducible protocol.
Mark

I'm not ignoring the long-range contribution, but yes, most of the
effects I am talking about are short-range. What I am asking is how much
the free energy of ionic hydration for K+ changes in, say, a system that
contains KCl in bulk water -- with and without autotuning. Hence also
the earlier question about being able to turn it off at least temporarily.
Alex

question

at hand?
Mark

Hi,
One needs to be more specific than NB. There is evidence that VDW

cutoffs

of traditional lengths cause approximation errors that cause

compensating

parameterization errors elsewhere; those effects get worse if the

system

inhomogeneous. Accordingly, mdrun never touches VDW cutoffs.

Electrostatic

with PME is quite another matter - there you need sufficient overall
accuracy, and there are multiple equivalent ways to do that.
Mark

understanding that NB stuff gets parameterized at a particular cutoff
value and our results are rather sensitive to that. I can't say we're
dying to have extreme repeatability, but is it in your opinion
acceptable to have variability in the cutoff radii and the rlist

between

something like 1.0 - 1.2 nm? To begin with, I am not particularly
worried about it, because we mostly report on qualitative behaviors,

but

I am interested in your opinion. I have read the manual and
unfortunately there is nothing in the way of actually showing

estimates

of NB energy variation as a function of small differences in cutoffs.
Thank you,
Alex

Hi,
There's quite detailed discussion of the treatment of pair searching

section 3.4.2 of the reference manual. Perhaps that clarifies things?

We're

not aware of a reason to want to control things manually, but if you

have

one, we're keen to hear of it!
Mark

Hi all,
We've long noticed that at the beginning of simulations mdrun goes

through

what seems like trying to adjust the short-range NB radii to its

liking.

What is up with that and does this mean that every simulation

proceeds

with

------------------------------
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Benson Muite

2018-12-07 06:01:06 UTC

Permalink

Dear Seketoulie,

Great. If replying to a digest, please change the subject so readers
know what is useful.

Regards,

Benson

Post by Seketoulie Keretsu
Dear
Thank you.
"yum install numpy" worked for me. Surprised why i haven't tried that long back.
On Fri, Dec 7, 2018 at 1:41 PM

inhomogeneous. Accordingly, mdrun never touches VDW cutoffs.

Electrostatic

with PME is quite another matter - there you need sufficient overall
accuracy, and there are multiple equivalent ways to do that.
Mark

Hi,
There's quite detailed discussion of the treatment of pair searching in
section 3.4.2 of the reference manual. Perhaps that clarifies things?

We're

not aware of a reason to want to control things manually, but if you

have

one, we're keen to hear of it!
Mark

Hi all,
We've long noticed that at the beginning of simulations mdrun goes

through

what seems like trying to adjust the short-range NB radii to its

liking.

What is up with that and does this mean that every simulation proceeds

with

question

at hand?
Mark

Hi,
One needs to be more specific than NB. There is evidence that VDW

cutoffs

of traditional lengths cause approximation errors that cause

compensating

parameterization errors elsewhere; those effects get worse if the

system

inhomogeneous. Accordingly, mdrun never touches VDW cutoffs.

Electrostatic

with PME is quite another matter - there you need sufficient overall
accuracy, and there are multiple equivalent ways to do that.
Mark

between

something like 1.0 - 1.2 nm? To begin with, I am not particularly
worried about it, because we mostly report on qualitative behaviors,

but

I am interested in your opinion. I have read the manual and
unfortunately there is nothing in the way of actually showing

estimates

of NB energy variation as a function of small differences in cutoffs.
Thank you,
Alex

Hi,
There's quite detailed discussion of the treatment of pair searching

section 3.4.2 of the reference manual. Perhaps that clarifies things?

We're

not aware of a reason to want to control things manually, but if you

have

one, we're keen to hear of it!
Mark

Hi all,
We've long noticed that at the beginning of simulations mdrun goes

through

what seems like trying to adjust the short-range NB radii to its

liking.

What is up with that and does this mean that every simulation

proceeds

with

--
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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