[gmx-users] The energy output code

Yang Ye leafyoung81-group at yahoo.com
Wed Jun 21 15:01:29 CEST 2006

Hi, Shao Qing

My view is same as Mark: such calculations need to be performed during
the MD

edr file only stores the calculated results arranged according to
groups. The content of edr file by g_energy is all what it has. To
restore the energy after MD is not very possible. Kinetic energy can not
be computed as usually velocity is not stored as frequently as
positions. Potential energy, unless only using cut-off, is not recoverable.

What Mark suggest, as I see, is the way to do it.

Yang Ye

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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