From: jagannath mondal <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: [email protected]
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.
Berk.
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