[gmx-users] Running MD only for selected part of molecule
vivek sharma
viveksharma.iitb at gmail.com
Fri Oct 17 08:02:59 CEST 2008
Hi Justin,
Thanks for your reply...
and apologies for asking you again.
If I want to keep a part of my molecule fix, say part out of 12 angstrom
radius from the ligand and also want to make avoid energy calculation for
the same, (using energy_excl)
Do I need to mention the separate group for that part of molecule, (as I
already did to make that part position restrained), and next how I will
mention those part in .mdp file...
Is it like...
energy_excl groupname protein/solvent (if I want to avoid energy
calculation between the group and protein/solvent)
or something else need to be done than that (like during genpr option).
Please explain....As I have no idea to play with such option...
My apologies again, if these small question irritates you.......
With Thanks,
Vivek
2008/10/15 Justin A. Lemkul <jalemkul at vt.edu>
>
>
> vivek sharma wrote:
>
>>
>> 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 ?
>>
>
> In the .mdp file.
>
> what are the other checks to be done for the same ?
>>
>>
> I don't know what you're asking.
>
> -Justin
>
> With Thanks,
>> Vivek
>> 2008/10/14 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>>
>>
>>
>> vivek sharma wrote:
>>
>>
>>
>> 2008/10/14 Justin A. Lemkul <jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu> <mailto: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>>
>> <mailto: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> <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 <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>>
>>
>>
> --
> ========================================
>
> 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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