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
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