[gmx-users] Calculating the energy of one molecule in themulti-molecule system

Yin Jian smayinj at nus.edu.sg
Fri Oct 12 16:03:46 CEST 2007

Hi Zhenhai,
anyway the bonded(bond lengths, bond angles, and dihedral angles) and 
nonbond energies can be calculated by hand with the geometry information

stored in pdb (xtc/trr) and the force field parameters. 

Jian Yin

Research Staff
Singapore-MIT Alliance (SMA)
National University of Singapore

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of shibalagu
Sent: Thursday, October 11, 2007 5:00 PM
To: gmx-users
Subject: [gmx-users] Calculating the energy of one molecule in
themulti-molecule system

Hi, all,

I did a simulation on a system which had more than one molecule in it.
After the simulation, I want to check the bond/angle/dihedral energy of
one molecule in the system.

So I set a energy_grp named DNA in the mdp file, and used the command
g_energy to calculate the energy on the energy_grp DNA. But I found that
if I set a energy_grp in the mdp file, I still can only calculate the
LJ/Coul energy on the molecule, and the bond/angle energy on the whole
system, without the bond or angle energy on the molecule separately. 

Does anyone can help me? Thanks a lot!

Li Zhenhai
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
Tel: 86-10-62773779
E-mail: shibalagu.thu at gmail.com


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