On 4/27/2011 4:02 PM, [email protected] wrote:
Dear all,
This question does not address issues of GROMACS development, and so
does not belong on gmx-developers. Please direct queries to the
appropriate forum. I am replying on the gmx-users list.
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?
The sum of the two parts of the PME approximation to the electrostatics
of an infinite periodic system has a connection to a physical
observable. There's no reason why one should expect the individual parts
to have one also.
Mark
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