[gmx-users] understanding of difference between gromacs procedures

[pragya chohan]

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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