[gmx-users] Re: g_enemat problem

Huafeng Xu huafeng at maxwell.compbio.ucsf.edu
Fri Mar 18 21:26:36 CET 2005

I just carried out the same calculation. Here is how to extract the energy 

1. Use make_ndx to build an index.ndx file for your system. For each group 
that you want to have energies computed, make a separate index for it. 
make_ndx has built-in help for selecting atom groups. By default, it will 
have three groups for your system: 1. [ System ] 2. [ Protein ] 3. [ Sol 
]. So if that is all you want, you don't have to make any selection. Just 
save and quit.

2. Edit your .mdp file, add or change the line
energygrp = Protein Sol MyGroups

3. grompp your mdp file with -n index.ndx -trr traj.trr -edr traj.edr 
options to make a rerun.tpr

4. run 
mdrun -s rerun.tpr -rerun traj.trr -e rerun.edr ...

5. Now use g_energy to look at your rerun.edr. You should be prompted to 
select from a list of energy components including the individual 
interactions betweeen your groups.

6. Relax and drink a beer.

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