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

[Justin A. Lemkul]

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

========================================