----- Original Message -----
From: Mahnam <[email protected]>
Date: Thursday, June 10, 2010 18:12
Subject: [gmx-users] combine position restraints and NPT equlibration in
membrane
To: [email protected]
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> > 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.
NPT equilibration with position restraints is not unreasonable, but if your
density is not correct, then your box needs to change size. Since the
position-restrained component can't change its coordinates much, you'll need to
equilibrate for a while to let other things rearrange around it.
Don't T-couple ions seperately. See
http://www.gromacs.org/Documentation/Terminology/Thermostats
Mark
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