[gmx-users] Force between groups

[Mark Abraham]

On 7/03/2010 4:24 PM, Michael McGovern wrote:
> Hi everyone. I have a trajectory file and for some analysis I'm doing I
> need to calcualte the force between two groups of atoms. Is there way to
> do this? Thank you.

Set up an index file for your groups (see webpage), use those groups as 
energy groups (see manual) in a suitable .mdp file with nstfout>0 (see 
manual), apply grompp with the aforementioned two files, then mdrun 
-rerun on the old trajectory with the new .tpr. There is no way to 
decompose energies or forces after the fact, even if you used nstfout != 
0 in the first place. This kind of procedure is exactly what mdrun 
-rerun is for.

Mark