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?> 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> > >
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========================================> > 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/> >
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