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

[Justin A. Lemkul]

vivek sharma wrote:
> 
> 
> 2008/10/14 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     vivek sharma wrote:
> 
>         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 ?
> 
> 
>     Position restraints do not necessarily guarantee that atomic
>     positions stay absolutely fixed.  Instead, there is an energy
>     penalty for moving them, which could in some cases be overcome.
> 
> 
>         I am not getting any idea of energy_excl option mentioned above,
>         please explain.
> 
> 
>     The freezegrps option can be used to fix atomic positions, but in
>     this case large forces can be generated within the frozen group.  As
>     such, you can apply energygrp_excl to exclude energetic terms within
>     the frozen group.
> 
> 
> Will it help me in reducing the time taken for the simulation if I'll 
> keep the part of molecule frozen ?
> 

I've never used freezegrps for any large set of atoms, so maybe.  If you've got 
surrounding solvent, though, the nonbonded interactions are still calculated 
between the frozen group and solvent, unless you turn that off too.  But then it 
starts getting really unphysical, in my view.

-Justin

> Thanks,
> ~Vivek
> 
> 
> 
>     -Justin
> 
>         With Thanks,
>         Vivek
> 
>         2008/10/12 Erik Lindahl <lindahl at cbr.su.se
>         <mailto:lindahl at cbr.su.se> <mailto:lindahl at cbr.su.se
>         <mailto: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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>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Graduate Research Assistant
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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