[gmx-users] problem with freeze-group : Large VCM(Berk Hess)

jagannath mondal jmondal2004 at yahoo.co.in
Sat May 12 20:18:46 CEST 2007

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 <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
> 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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