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

[Mark Abraham]

----- Original Message -----
From: Mahnam <mahnam at ibb.ut.ac.ir>
Date: Thursday, June 10, 2010 18:12
Subject: [gmx-users] combine position restraints and NPT equlibration in membrane
To: gmx-users at gromacs.org


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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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