From: jagannath mondal <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
Subject: RE: [gmx-users] problem with freeze-group : Large VCM(Berk Hess)
Date: Sat, 12 May 2007 19:18:46 +0100 (BST)
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.
Sorry, I missed this email.
I assume cmm-mode is a typo only in your mail, not in your mdp file.
In principal frozen atoms should not move.
However, if you are freezing part of a molecule and there are
free groups connected with constraints to the frozen group,
you could have some motion.
But from your mail it seems like something else is wrong.
Why do you want to freeze part of a molecule?
Wouldn't position restraints be a better approach?
Berk.
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