Quoting pragya chohan <[EMAIL PROTECTED]>: > > > Thanks for your reply. Can you tell me which one is a better way for carrying > out the simulation?
Search the literature regarding membrane protein MD to see what types of protocols people are using, and how accurate their results are. -Justin > > ---------------------------------------- > > Date: Mon, 17 Mar 2008 09:13:03 -0400 > > From: [EMAIL PROTECTED] > > To: [email protected] > > Subject: RE: [gmx-users] understanding of difference between gromacs > procedures > > > > 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 > > _________________________________________________________________ > Tried the new MSN Messenger? ItÂ’s cool! Download now. > http://messenger.msn.com/Download/Default.aspx?mkt=en-in_______________________________________________ > 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
