Hi Berk,
Thanks a lot for your reply. According to your
suggestion, I did not remove the cmm for the WHOLE
molecule i.e I used 'cmm-mode=None'for the
entire system. (Did you mean that I should have
removed the restriction only for freeze-group or for
whole system?)
But now I have two problems:
1) the simulation is now going for longer time but
finally again crashes.
2) I freezed the mainchain because I did not want
the mainchain
move at all and I wanted the only side-chain move. But
, when I am
visualising the trajectory in VMD, I am finding that
whole molecule is
tumbling including the main-chain i.e the whole
molecule is changing
its position. As ususal, I did not use pressure
coupling . Do you think that the movement of whole
molecule is expected during freeze group simulation?
should I modify something else in my parameter file?
I am again giving the .mdp file.
--- Berk Hess [EMAIL PROTECTED] wrote:
From: jagannath mondal [EMAIL PROTECTED]
Reply-To: Discussion list for GROMACS users
gmx-users@gromacs.org
To: gmx-users@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.
Berk.
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