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

Berk Hess gmx3 at hotmail.com
Wed May 23 12:24:50 CEST 2007

>From: jagannath mondal <jmondal2004 at yahoo.co.in>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>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?


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