[gmx-users] understanding of difference between gromacs procedures

[Justin A. Lemkul]

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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