[gmx-users] The energy output code

Uwe Richter urichter at jerini.de
Wed Jun 21 13:37:21 CEST 2006


I'd rather resort to the following.

Extract each single frame from your trajectory.
Check whether your criteria for including certain atoms/indices are
Create a separate index file for each frame.
Recalculate the energy.

With some scripting ability this approach could be automatized easily.

Best regards,

Shao Qing wrote:

> Thanks Mark for your reply. I think I have not express myself clearly.
> I do not plan to do this during the MD run but after the MD run.
> For example, I have two groups
> A 1 2 3 4
> B 5 6 7 8
> I want to calculate the enery between group A and group B, but need
> some additive criterion to make sure, say, the interaction enery
> between 1 and 5 should be added to the sum or not.
> I wish to find the energy code of the gmx to output edr, then maybe I
> can modified it.
> I still cannot find the src code of the subroutine.
> Or any other good method?
> Thanks
> >>Shao Qing wrote:
> >> Gromacsers:
> >> Hello, everyone. I want to calculate the interaction energy of
> molecules in certain region, like in the pore. Because the molecules
> can move inside the pore and outside it. A group is not suitable here,
> I guess. I do not find such tools in the gmx_tools, either. I want to
> change the code of the subroutine output energy in the mdrun to
> fulfill my aim. Could anyone tell me where the subroutine is? I mean,
> the subroutine to calculate the energy in the mdrun and output it to
> the edr.
> >> Thanks in advance
> Mark wrote
> > Caveat, I'm not expert enough to be sure what I'm saying is right, but I
> think it right!
> > It's not as simple as that. The energies (and forces) are computed
> group-wise, so you need to construct a group back in the .top file
> before evaluating the energy. The simplest way to do that would be to
> decided in advance how many water molecules will be in the group, and at
> each energy output step, recompute exactly which water molecules are
> close enough to be part of the group, and fill the group data structure
> with the corresponding indices. Then magically the energy for that group
> will be calculated and appear in the .edr output.
> > Mark
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