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

[vivek sharma]

2008/10/14 Justin A. Lemkul <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 ?

Thanks,
~Vivek

>
>
> -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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>
> --
> ========================================
>
> 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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