[gmx-users] problem with freeze-group : Large VCM

Berk Hess gmx3 at hotmail.com
Fri May 11 14:50:51 CEST 2007

>From: jagannath mondal <jmondal2004 at yahoo.co.in>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] problem with freeze-group : Large VCM
>Date: Fri, 11 May 2007 00:19:53 +0100 (BST)
>Hi Gromacs user,
>      I am a gromacs beginner struggling with
>freeze-group simulation.
>  I was trying to simulate a beta-peptide(un-natural
>peptide ) by relaxing only the side-chains but I am
>getting error regarding large VCM and
>The system has only 1 peptide (14-residue ) and No
>solvent.  So, for this purpose , I generated a
>freeze-group which contains all the main-chain atoms.
>Initially I was using pressure-coupling and it was
>giving error in simulation.   Later   I found many
>discussion on this freeze-group simulation in
>user-archive and manual and  accordingly
>   I did not use pressure-coupling in my simulation
>and before the simulation, I minimised my peptide
>using steep
>  integrator and then  with the minimised structure I
>tried a MD run. But after 40 ps, the mdrun crashes
>with complaint about nsgrid and large VCM:

You should not remove com motion when using freeze groups,
since the com is no longer free to move.

We should let grompp print a warning for this.


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