[gmx-users] RE:

Ilya Chorny ichorny at maxwell.compbio.ucsf.edu
Sun Mar 14 17:54:01 CET 2004

This has been done many times before in the literature. The simplest naive
way to do is just to run 
an equillibrium simulation and calcualte P(phi,psi). If you want to get to
phi psi angles which are 
not accessable on the time scale of your simulation then you will have to
use a restraining potential inored to
explore a region of torsional space. This is called umbrella sampling and I
believe gromacs has implimented
some umbrella sampling but I'm note sure if they allow for  torsional


-----Original Message-----
From: Mungikar, Amol Arvind (UMR-Student)
[mailto:gmx-users-admin at gromacs.org]On Behalf Of Mungikar, Amol Arvind
Sent: Saturday, March 13, 2004 5:18 PM
To: gmx-users at gromacs.org

Dear all,
I was wondering if anybody has used gromacs for calculation of free energy
surface of the protein as a function of phi and psi (torsional angles). If
yes kindly let me know if this is possible, or I have to make some changes
to the source code.
Thank you very much in advance!

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