Dear Mark:
Thanks a lot for all the suggestions. They are really illuminating.
Sincerely,
Bin
On Mar 26, 2010, at 5:56 PM, Mark Abraham wrote:
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
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