[gmx-users] understanding of difference between gromacs procedures

[pragya chohan]

Thanks for your reply. Can you tell me which one is a better way for carrying out the simulation?

----------------------------------------
> 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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