[gmx-users] understanding of difference between gromacs procedures

[Justin A. Lemkul]

Quoting pragya chohan <pragyachohan at hotmail.com>:

>
>
> 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: 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>:
> >
> > >
> > > 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: 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> > >
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> > > ========================================> > 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/> >
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> > ========================================
> >
> > 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/
> >
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========================================

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/

========================================