[gmx-users] Running MD only for selected part of molecule
Samuel Coulbourn Flores 花山
scflores at stanford.edu
Fri Oct 10 19:22:35 CEST 2008
You might want to try Simbody (simtk.org). This will allow you to
rigidify any part or parts of the molecule you choose. As a bonus,
you will not spend resources computing intramolecular interactions in
the rigidified regions.
Sam
On Oct 10, 2008, at 6:10 AM, Justin A. Lemkul wrote:
>
>
> vivek sharma wrote:
>> Hi justin,
>> My apologies for asking you so many small queries.
>> Can you suggest any good tutorial or reference that talks about
>> this issue of running MD over a selected part of molecule.
>
> If you're using PR, all you're doing is position-restrained dynamics.
>
> -Justin
>
>> With Thanks,
>> Vivek
>> 2008/10/10 vivek sharma <viveksharma.iitb at gmail.com <mailto:viveksharma.iitb at gmail.com
>> >>
>> hI justin,
>> Thanks for your response.
>> do I need to specify the index file(for residue that I want to
>> keep
>> fix during MD) during GROMPP or just including the psre.itp in
>> topology is enough for the purpose ?
>> With Thanks,
>> Vivek
>> 2008/10/10 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu
>> >>
>> Justin A. Lemkul wrote:
>> vivek sharma wrote:
>> Thanks Justin,
>> My goal is to keep certain part fixed and move only a
>> few of the residues (case is like providing
>> flexibility
>> to the site of interest only).
>> SO , do I need to specify the residue using some index
>> file ?
>> or is there some other way to specify the part of
>> molecule for position restraining ??
>> Make an index file with the residues you want to keep fixed,
>> and
>> pass it
>> to genpr to generate a new posre.itp that corresponds to those
>> residues.
>> -Justin
>> With Thanks,
>> Vivek
>> 2008/10/10 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 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.
>> -Justin
>> With Thanks,
>> Vivek
>>
>> ------------------------------------------------------------------------
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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
>> ========================================
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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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Samuel Coulbourn Flores, PhD
Altman Lab
Department of BioEngineering
Stanford University
samuel.flores at aya.yale.edu
650.644.8416
花山
科学者
生物工学部
スタンフォ一ド大学
スタンフォ一ド、カリフォルニア、米国
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