[gmx-users] General MD question

Carsten Kutzner ckutzne at gwdg.de
Tue Feb 1 09:58:07 CET 2011

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)?


> Grüsse
> Stephan Watkins
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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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