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 ??
With Thanks, Vivek 2008/10/10 Justin A. Lemkul <[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 >> 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 >> > > -- > ======================================== > > 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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