[gmx-users] Re:General MD question

Carsten Kutzner ckutzne at gwdg.de
Wed Feb 2 14:26:06 CET 2011

On Feb 2, 2011, at 11:48 AM, lloyd riggs wrote:

> Dear Carsten Kutzner,
> First off, thanks.  I did not specify it in the input md.mdp file, but when I looked at the generated out.mdp it had a Linear center of mass removal for the groups [system].
> When I added the pull vector it works, untill the two subunits crash(move past a realistic distance towards eachother and the force ==too much, and then it crashes after atoms fly off....but I get a change in dG up untill this point from solution.
> I will try and play around today, but woundered if anyone could spot check my final .mdp input, as I lack in reviewers (for this portion of
I or somebody else can take a quick look for any obvious issues, but
nobody can guarantee the correctness of what you get, of course.
This is entirely your responsibility.


> my work, ie people using gromacs).  As at some distant point in time I will try and publish dG/ dH and possibly dS, and relate these to affinities (Ka, KD and kD), I would like to make sure I did it correctly before the hellish number crunching(ie most time consuming) part.  I did look over the tutorial already...
> Thanks
> Stephan Watkins
> Message: 3
> Date: Tue, 1 Feb 2011 09:58:07 +0100
> From: Carsten Kutzner <ckutzne at gwdg.de>
> Subject: Re: [gmx-users] General MD question
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <D4F55DFA-019A-43C4-9811-63FB4FD6E463 at gwdg.de>
> Content-Type: text/plain; charset=iso-8859-1
> Hi Stephan,
> On Jan 31, 2011, at 5:18 PM, lloyd riggs wrote:
>> Dear All,
>> A quick question as I have not really delved into code for gromacs ever, nor know anyone close whom has worked on it.
>> If I set up an MD simulation using a 4 protein complex, and 1 small peptide, plus waters, etc...and run the whole thing the proteins never move, only the amino acids within(constant temp RT and pressure 1 bar).
>> Two domains make one complex, and another two the other.  Basically, if I seperate the domains say 5, 10, 15 angstrom, etc...the amino acids will drift (the chains) towards each other, but the two large (global) protein units never move their center (I know I can make it work with Pull vectors, but why not in the simple system with a generated initial randomized velocities), I woundered why they are fixed in a normal run with minimal parameters?  Is there a reason (specific to developers), historical reason, or other?  As waters move around fine, and anything else added (salt, small molecules of 20-30 atoms, water) except the central molecule(s) of interest.
> In a 'normal' run they should not be fixed. Could it be that you did accidentally
> fix them by specifying center of mass removal (comm-grps in .mdp)?
> Carsten
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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