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

vivek sharma viveksharma.iitb at gmail.com
Wed Oct 15 09:14:45 CEST 2008


Dear Justin,
Thanks for your reply..
But I am not getting how and where should I give the option of energy_excl.
For freezing a part of molecule ?
what are the other checks to be done for the same ?

With Thanks,
Vivek
2008/10/14 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> 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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