[gmx-developers] Read the component energy and force from the code during simulation

Berk Hess hess at kth.se
Wed Sep 7 12:17:34 CEST 2016


Please don't send the same mail multiple times.

Your request is not clear enough. Do you want forces on different parts 
of the system or between different parts of the system? The latter is 
difficult to obtain.
Note that with PME, which is what you should be using in most cases, it 
is difficult, if not impossible, to decompose forces and energies 
between group (pairs).



On 2016-09-07 11:46, Yi Isaac Yang wrote:
> Dear developers,
> I am developing an enhanced sampling method, and I have already 
> realized it in AMBER. Now I want to add the code of this method into 
> Gromacs. This method need to read the component energy and force of 
> different part of the system (like protein, solution, etc.) during the 
> simulation. However, I am not very familiar withe the codes of 
> Gromacs, so I don't know how to read it. I know when I perform MD 
> simulation using Gromacs I can set the groups in "energygrps", then I 
> can read the energy between those groups in .edr file. So I think it 
> shouldn't be too difficult to read the component energy and force in 
> the codes. Can you tell me how to read the component energy and force 
> from the codes?
> Thank you very much and best regards,
> Isaac

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