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

[Justin A. Lemkul]

vivek sharma wrote:
> 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 ?

No; you just need it to pass to genpr.

Please remember to copy the list on your questions and responses!

-Justin

> 
> 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
> 
> 
>                  
>              ------------------------------------------------------------------------
> 
>                    _______________________________________________
>                    gmx-users mailing list    gmx-users at gromacs.org
>             <mailto:gmx-users at gromacs.org>
>                    <mailto:gmx-users at gromacs.org
>             <mailto:gmx-users at gromacs.org>>
>                    http://www.gromacs.org/mailman/listinfo/gmx-users
>                    Please search the archive at
>             http://www.gromacs.org/search
>                    before posting!
>                    Please don't post (un)subscribe requests to the list.
>             Use the
>                    www interface or send it to
>             gmx-users-request at gromacs.org
>             <mailto:gmx-users-request at gromacs.org>
>                    <mailto:gmx-users-request at gromacs.org
>             <mailto:gmx-users-request at gromacs.org>>.
>                    Can't post? Read
>             http://www.gromacs.org/mailing_lists/users.php
> 
> 
>                --     ========================================
> 
>                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
> 
>                ========================================
>                _______________________________________________
>                gmx-users mailing list    gmx-users at gromacs.org
>             <mailto:gmx-users at gromacs.org>
>                <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>                http://www.gromacs.org/mailman/listinfo/gmx-users
>                Please search the archive at
>             http://www.gromacs.org/search before
>                posting!
>                Please don't post (un)subscribe requests to the list. Use
>             the www
>                interface or send it to gmx-users-request at gromacs.org
>             <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>             <mailto:gmx-users-request at gromacs.org>>.
>                Can't post? Read
>             http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
> 
>     -- 
>     ========================================
> 
>     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
> 
>     ========================================
>     _______________________________________________
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://www.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/search before
>     posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
> 
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 

-- 
========================================

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

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