[gmx-users] problem with freeze-group : Large VCM(Berk Hess)
jmondal2004 at yahoo.co.in
Sat May 12 20:18:46 CEST 2007
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
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
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 <gmx3 at hotmail.com> wrote:
> >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
> >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
> >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
> >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
> since the com is no longer free to move.
> We should let grompp print a warning for this.
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