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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?<BR><BR>> Date: Mon, 17 Mar 2008 08:30:49 -0400<BR>> From: jalemkul@vt.edu<BR>> To: gmx-users@gromacs.org<BR>> Subject: RE: [gmx-users] understanding of difference between gromacs procedures<BR>> <BR>> Quoting pragya chohan <pragyachohan@hotmail.com>:<BR>> <BR>> ><BR>> > One of my lab-mates<BR>> > > > is doing the same system by following a different procedure (difference<BR>> > > > listed below)<BR>> > > > I did position restrain by define = -DPOSRES -DPOSRES_LIPID<BR>> > > > and he is doing define = -DPOSRES<BR>> > > > and then for lipid.<BR>> > ><BR>> > > I don't understand what you mean by this.<BR>> > one of us are putting restrain on both protein and lipid and removing<BR>> > restrain from first lipid while keeping force on the protein and then<BR>> > removing restrain from protein whereas other one is only putting restrain on<BR>> > protein first and after removing the restrain from protein then applies<BR>> > restrain to the lipid .<BR>> <BR>> So one approach is to progressively remove restraints, while the other seems to<BR>> remove restraints and add them back on in different groups. I would think the<BR>> more correct approach would be the first, but you still haven't told us what<BR>> step this is. Minimization? Equilibration?<BR>> <BR>> It seems to me that if this is an equilibration, you are certain to see<BR>> differences, as Mark has already pointed out. If this is a minimization, the<BR>> second procedure of removing and re-adding restraints seems to make no sense to<BR>> me.<BR>> <BR>> -Justin<BR>> <BR>> > > > Rest of the procedure is the same.<BR>> > > > He got conformational change within 250 ps and I did not get till 2ns<BR>> > > > even though we use same parameters on mdp and have same starting<BR>> > structure.<BR>> > > ><BR>> > > > Can anyone give some insight what may be the logic for this difference?<BR>> > ><BR>> > > If one of you is position-restraining your lipids and one isn't, surely<BR>> > > the fact that you get conformational change at a different time is<BR>> > expected.<BR>> > ><BR>> > > You've also not said whether anybody is removing position restraints at<BR>> > > any stage of the MD.<BR>> > ><BR>> > > Mark<BR>> > > _______________________________________________<BR>> > > gmx-users mailing list gmx-users@gromacs.org<BR>> > > http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> > > Please search the archive at http://www.gromacs.org/search before posting!<BR>> > > Please don't post (un)subscribe requests to the list. Use the<BR>> > > www interface or send it to gmx-users-request@gromacs.org.<BR>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>> ><BR>> > _________________________________________________________________<BR>> > Post free property ads on Yello Classifieds now! www.yello.in<BR>> ><BR>> http://ss1.richmedia.in/recurl.asp?pid=220_______________________________________________<BR>> > gmx-users mailing list gmx-users@gromacs.org<BR>> > http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> > Please search the archive at http://www.gromacs.org/search before posting!<BR>> > Please don't post (un)subscribe requests to the list. Use the<BR>> > www interface or send it to gmx-users-request@gromacs.org.<BR>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>> ><BR>> <BR>> <BR>> <BR>> ========================================<BR>> <BR>> Justin A. Lemkul<BR>> Graduate Research Assistant<BR>> Department of Biochemistry<BR>> Virginia Tech<BR>> Blacksburg, VA<BR>> jalemkul@vt.edu | (540) 231-9080<BR>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/<BR>> <BR>> ========================================<BR>> _______________________________________________<BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the <BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR><br /><hr />It's about getting married. Click here! <a href='http://ss1.richmedia.in/recurl.asp?pid=201' target='_new'>Try it!</a></body>
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