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

[Justin A. Lemkul]

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.

-Justin

> With Thanks,
> Vivek
> 
> 2008/10/12 Erik Lindahl <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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-- 
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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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