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<DIV><FONT face=Verdana color=#0000ff size=2>
<DIV>Thanks Mark for your reply. I think I have not express myself
clearly. </DIV>
<DIV> I do not plan to do this during the MD run but after the MD
run. </DIV>
<DIV>For example, I have two groups </DIV>
<DIV>A 1 2 3 4 </DIV>
<DIV>B 5 6 7 8</DIV>
<DIV>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. </DIV>
<DIV>I wish to find the energy code of the gmx to output edr, then maybe I can
modified it.</DIV>
<DIV>I still cannot find the src code of the subroutine.</DIV>
<DIV>Or any other good method?</DIV>
<DIV>Thanks</DIV>
<DIV>>>Shao Qing wrote:</DIV>
<DIV>>> Gromacsers: </DIV>
<DIV>>> 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.</DIV>
<DIV>>> Thanks in advance </DIV>
<DIV>
<DIV>Mark wrote</DIV></DIV>
<DIV>> Caveat, I'm not expert enough to
be sure what I'm saying is right,
but I</DIV>
<DIV>think it right!</DIV>
<DIV> </DIV>
<DIV>> It's not as simple as that. The
energies (and forces) are computed</DIV>
<DIV>group-wise, so you need to construct a
group back in the .top file</DIV>
<DIV>before evaluating the energy. The simplest
way to do that would be to</DIV>
<DIV>decided in advance how many water
molecules will be in the group, and
at</DIV>
<DIV>each energy output step, recompute exactly
which water molecules are</DIV>
<DIV>close enough to be part of the
group, and fill the group data
structure</DIV>
<DIV>with the corresponding indices. Then
magically the energy for that group</DIV>
<DIV>will be calculated and appear in the
.edr output.</DIV>
<DIV> </DIV>
<DIV>> Mark</DIV></FONT></DIV>
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<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>------------------------------</DIV>
<DIV> </DIV>
<DIV>_______________________________________________</DIV>
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<DIV> </DIV>
<DIV>End of gmx-users Digest, Vol 26, Issue
74</DIV>
<DIV>*****************************************</DIV></FONT></DIV></BODY></HTML>