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 <[EMAIL PROTECTED]> > > > 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 <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> >>> >>> >>> >>> 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@gromacs.org >>> <mailto:gmx-users@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 [EMAIL PROTECTED] >>> <mailto:[EMAIL PROTECTED]>. >>> 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@gromacs.org >>> <mailto:gmx-users@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 [EMAIL PROTECTED] >>> <mailto:[EMAIL PROTECTED]>. >>> 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 > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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