[gmx-users] Energy minimization by keeping heavy atom fixed

Mark Abraham mark.abraham at anu.edu.au
Thu Aug 26 09:15:49 CEST 2010

----- Original Message -----
From: priyabrata panigrahi <priyabrata0 at gmail.com>
Date: Thursday, August 26, 2010 17:09
Subject: [gmx-users] Energy minimization by keeping heavy atom fixed
To: gmx-users at gromacs.org

> I have a protein structure determined by x-ray crystallography method where hydrogen atoms were missing. I have added hydrogen atom. Now i need to do energy minimization of this protein by keeping the heavy atom fixed at their crystallographic position. How can I manage which atoms to be fixed and which to keep flexible during EM and MD.

 The mechanism is called "position restraints" and you should read about that in the manual. pdb2gmx will help generate the necessary file.


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