[gmx-users] output forces between group of atoms
Mark.Abraham at anu.edu.au
Sat Mar 27 01:56:44 CET 2010
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.
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