[gmx-developers] positive Coulomb LR potential for 100 A molecules system, A is positive molecules!

huzhongqiao at gmail.com huzhongqiao at gmail.com
Wed Apr 27 08:02:49 CEST 2011

Dear all,

I am calculating the interaction between A and B, where A is positive
molecule, B is negative molecule. What I have done is as follows. First I
run MD for the system A+B, which consists of 100 A molecules and 100 B
molecules respectively, and the whole system is neutral. After MD, I exact
trajectory of only 100 A molecules and only 100 B molecules. So now I have
three trajectories, 100A, 100B, 100A+100B. Then I use -rerun flag in mdrun
command to get potential E of these three systems respectively. The
interaction dE between A and B is calculated using the equation dE =
E(100A+100B)-E(100A)-E(100B). The value obtained is seemingly reasonable.
But when I check the potential compoents, i.e, LJSR, CoulombSR, CoulombLR
(or Coul. recip.) terms, one problem is arising. I find the CoulombLR is
positive for system 100A. According to my understanding, A is positive and A
molecules are repulsive to each other, and so the system of 100 A molecules
should have positive CoulombLR potential. But mdrun -rerun for 100A system
give negative CoulombLR potential. In MD run, I used PME for coulomb LR
interadtion. Is this the reason? Anybody can help explain this?

Thanks in advance,

Zhongqiao Hu
Research Fellow
Dept of Chem Biomol Eng
National University of Singapore
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