[gmx-users] Running MD only for selected part of molecule

vivek sharma viveksharma.iitb at gmail.com
Tue Oct 14 12:00:33 CEST 2008

Hi there,

I tried the mdrun by keeping a group of residue position restrained, and it
is working well (verified by comparing RMSD plot for the same), thanks for
your suggestions regarding the same.
But, I have seen that the part of the molecule I kept for PR is still having
some motion, how can I keep that part rigid ?
I am not getting any idea of energy_excl option mentioned above, please

With Thanks,

2008/10/12 Erik Lindahl <lindahl at cbr.su.se>

> Hi,
> On Oct 10, 2008, at 12:46 PM, Justin A. Lemkul wrote:
>>> I want to run MD over a part of my molecule , for few residues only (not
>>> the whole molecule).
>>> Can I do it using GROMACS ?
>>> I searched for the online documentation and mailing list, but unable to
>>> get appropriate information.
>>> If somebody has already tried such things earlier, please suggest and
>>> direct me for appropriate link and address.
>> Well, if your goal is to keep certain parts fixed and allow others to
>> move, probably the easiest way to do it is to apply position restraints to
>> the "fixed" part.
> You can also set parts of the system as a freeze group, in which case you
> can exclude all nonbonded interactions inside the freeze group with the
> energygrp_excl option in your mdp file.
> The main advantage of this is of course that you will improve performance
> if 99% of your system is frozen (although all interactions between the
> frozen and non-frozen parts still have to be calculated). On the other hand,
> completely freezing part of the system is not very realistic, and you're
> likely to get strange behavior in the interface...
> Cheers,
> Erik
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