[gmx-users] understanding of difference between gromacs procedures

pragya chohan pragyachohan at hotmail.com
Mon Mar 17 13:07:48 CET 2008

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 .
> > 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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