[gmx-users] understanding of difference between gromacs procedures

pragya chohan pragyachohan at hotmail.com
Mon Mar 17 13:39:55 CET 2008


the step is indeed equillibration ... thanks for the reply .... so can we say that the second step will produce entirely different results throughout or will it be a matter of only time of simulation needed?> Date: Mon, 17 Mar 2008 08:30:49 -0400> From: jalemkul at vt.edu> To: gmx-users at gromacs.org> Subject: RE: [gmx-users] understanding of difference between gromacs procedures> > Quoting pragya chohan <pragyachohan at hotmail.com>:> > >> > One of my lab-mates> > > > is doing the same system by following a different procedure (difference> > > > listed below)> > > > I did position restrain by define = -DPOSRES -DPOSRES_LIPID> > > > and he is doing define = -DPOSRES> > > > and then for lipid.> > >> > > I don't understand what you mean by this.> > one of us are putting restrain on both protein and lipid and removing> > restrain from first lipid while keeping force on the protein and then> > removing restrain from protein whereas other one is only putting restrain on> > protein first and after removing the restrain from protein then applies> > restrain to the lipid .> > So one approach is to progressively remove restraints, while the other seems to> remove restraints and add them back on in different groups. I would think the> more correct approach would be the first, but you still haven't told us what> step this is. Minimization? Equilibration?> > It seems to me that if this is an equilibration, you are certain to see> differences, as Mark has already pointed out. If this is a minimization, the> second procedure of removing and re-adding restraints seems to make no sense to> me.> > -Justin> > > > > Rest of the procedure is the same.> > > > He got conformational change within 250 ps and I did not get till 2ns> > > > even though we use same parameters on mdp and have same starting> > structure.> > > >> > > > Can anyone give some insight what may be the logic for this difference?> > >> > > If one of you is position-restraining your lipids and one isn't, surely> > > the fact that you get conformational change at a different time is> > expected.> > >> > > You've also not said whether anybody is removing position restraints at> > > any stage of the MD.> > >> > > Mark> > > _______________________________________________> > > gmx-users mailing list 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.> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php> >> > _________________________________________________________________> > Post free property ads on Yello Classifieds now! www.yello.in> >> http://ss1.richmedia.in/recurl.asp?pid=220_______________________________________________> > gmx-users mailing list 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.> > 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 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.> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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