[gmx-users] Calculateing LJ and electrostatic energies

Jochen Hub jhub at gwdg.de
Mon Feb 13 16:13:10 CET 2006

hnam wrote:

> In the name of God
> Hello gmx-users
> Would you please tell me how I can calculate LJ and electrostatic and 
> ... energies for *each* amino acids of my protein with Gromacs ?

You need to create an index file with appropriate groups, write the 
groups behind "energygrps" in your mdp file (they must not overlap) and 
use g_energy with the edr file after the run.

good luck, Jochen

> Thank you very much in advance
> Institute of  Biochemistry  and  Biophysics (IBB)
> Tehran University
> P.O.box 1417614411
> Tehran
> Iran
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Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de

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