[gmx-users] output forces between group of atoms

[BIN ZHANG]

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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