[gmx-users] PR EM

Itamar Kass ikass at cc.huji.ac.il
Wed Jan 5 07:23:39 CET 2005

   Hi, when you produce the top files pdb2gmx also produced files such 
as posre_*.itp, which can be used to fixed the protein.  In your em.mdp 
file add the line
"define               = -DPOSRES".
   The above is technically true, but theoretically EM upon a system is 
done when atoms do not have any kinetic energy, hence if you protein is 
totally  minimize no change will happen.  If changes accrue this mean 
your protein is not well minimized.
    Have a nice day, Itamar.

On Jan 4, 2005, at 9:50 PM, Alberto Malvezzi wrote:

> Dear collegues,
> how to make gromacs perform an energy minimization of water molecules 
> but keeping the protein atoms fixed?
> Thanks
> Alberto
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| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585146
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