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
>
> >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.
>
>
_
> Play online games with your friends with Messenger
> http://www.join.msn.com/messenger/overview
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the
> list. Use the
> www interface or send it to
> [EMAIL PROTECTED]
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
Office firewalls, cyber cafes, college labs, don't allow you to download
CHAT? Click here: http://in.messenger.yahoo.com/webmessengerpromo.php
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php