[gmx-users] combine position restraints and NPT equlibration in membrane

Justin A. Lemkul jalemkul at vt.edu
Sat Jun 12 02:58:59 CEST 2010

Quoting Mahnam <mahnam at ibb.ut.ac.ir>:

> In God We Trust
> Hello Dear GMX users
> We would like to perform  MD simulation of a protein in attendance of
> biomembrane (POPE). On the basis of Kalp tutorial, can we combine position
> restraints and NPT  equlibration in one phase?. We attached NPT.mdp in this
> mail.  Please guide us.

In the tutorial, position restraints are applied during both NVT and NPT
equilibration, with the purpose of separately equilibrating temperature and
pressure.  You could try to do both in one NPT run, but in my experience, POPE
requires some finesse during equilibration, so two phases are probably best.


> Many thanks in advance for your help and your reply.
> Yours truly
> Karim Mahnam
> Institute of  Biochemistry  and  Biophysics (IBB)
> Tehran University
> P.O.box 13145-1384
> Tehran
> Iran
> http://www.ibb.ut.ac.ir/


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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