[gmx-users] output forces between group of atoms
zhngbn at gmail.com
Sun Mar 28 21:01:45 CEST 2010
Thanks a lot for all the suggestions. They are really illuminating.
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
> 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
>> 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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