Quoting pragya chohan <[EMAIL PROTECTED]>: > > 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?
Well, it's hard to say definitively, but if you want to replicate results and are preparing your systems differently, I wouldn't count on getting anything that correlates. -Justin > Date: Mon, 17 Mar > 2008 08:30:49 -0400> From: [EMAIL PROTECTED]> To: [email protected]> > Subject: RE: [gmx-users] understanding of difference between gromacs > procedures> > Quoting pragya chohan <[EMAIL PROTECTED]>:> > >> > 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 > [email protected]> > > 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> >> > > _________________________________________________________________> > Post > free property ads on Yello Classifieds now! www.yello.in> >> > http://ss1.richmedia.in/recurl.asp?pid=220_______________________________________________> > > gmx-users mailing list [email protected]> > > 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> [EMAIL PROTECTED] | (540) 231-9080> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/> > > ========================================> > _______________________________________________> gmx-users mailing list > [email protected]> 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 > _________________________________________________________________ > Post free property ads on Yello Classifieds now! www.yello.in > http://ss1.richmedia.in/recurl.asp?pid=219 ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] 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
