hi Justin, Thanks for your reply... I am interested in looking for the stability of the docked pose, by applying some temperature variation in the molecule. If I am applying temperature variation then should I use pressure coupling simultaneously. Can you suggest some tutorial for such attempts.....
With Thanks, Vivek 2008/11/10 Justin A. Lemkul <[EMAIL PROTECTED]> > > > vivek sharma wrote: > >> Hi There, >> I am running MDS over the docked poses to check the stability of the >> docked poses using gromacs. >> I have few doubts about selecting parameters for the same, If anybody have >> tried such thing earlier, please suggest me for the same. >> >> Should I keep pressure coupling over the simulation ? >> > > Sure; life exists at NPT, so it is commonly used in routine protein > simulations. > > For how long should I run the simulation for such purpose ? >> >> > That's up to you :) You should run the simulations as long as you feel > necessary to achieve stability. I know that's vague, but there really is no > single correct answer to this question in the MD field. If there is, I'd > love for someone to tell me, too...;) > > -Justin > > Waiting for suggestions. >> >> 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 >
_______________________________________________ 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