[gmx-users] PME Coulomb Long Range contributions

David van der Spoel spoel at xray.bmc.uu.se
Fri Nov 25 11:05:53 CET 2005

MyTaira wrote:

> 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?

Yes, you have to use mdrun -rerun, check mailing list archives.

> Thank you,
> Igor
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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