[gmx-users] output forces between group of atoms

[Mark Abraham]

On 27/03/2010 8:24 AM, BIN ZHANG wrote:
> Dear all:
>
> In gromacs, is it possible to output forces between two groups of atoms?

Yes. Run a trajectory, keep only the frames you wish to analyse, and 
then use mdrun -rerun on that trajectory with a modified .mdp file. That 
.mdp file should make suitable use of energy groups and energy group 
exclusions so that you only calculate the forces you want.

> Or is it possible to decompose forces into separate parts, like for LJ,
> and electrostatics?

You can use "user tables" to achieve this. See manual 6.7. 
Alternatively, re-define the relevant parameters to zero in one or more 
reruns, as above, to achieve the decomposition.

Mark