[gmx-users] PME Coulomb Long Range contributions
mytaira at yandex.ru
Fri Nov 25 09:57:34 CET 2005
Hello, gromacs user community!
My simulated system consist of solute (SLT) 1 molecule (46 atoms) and
solvent n-hexane (HEX) 250 molecules (5000 atoms). I use PME method for
treatment of long range Coulomb. The value of the Coulomb interaction energy
between the solute and solvent (SLT-HEX) for each MD configuration is
necessary for my research.
So in this goal I specified two energy groups (SLT, HEX) in energygrp.
Energy contributions for each configuration are saved in ener.edr file.
After simulation I extracted Coulomb terms [Coul(SR) and Coul(LR)] from
ener.edr file using g_energy program. There is energy group matrix 2x2 of
contributions SLT-SLT, SLT-HEX, HEX-SLT and HEX-HEX for both the Coul(SR)
and Coul(LR) terms. The energy group matrix for Coul(SR) term has valid
values of elements. But the matrix for Coul(LR) term has only zero-values.
How do obtain right values of energy group matrix for Coul(LR) term
[particularly Coul(LR): SLT-HEX] in PME long range treatment?
Is it possible without programming?
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