[gmx-users] PME Coulomb Long Range contributions

MyTaira 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?
Thank you,

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