[gmx-users] Help to interpret the energy terms for gmx energy

Jose teruel at um.es
Tue Dec 5 17:10:47 CET 2017

Hi all,

My simulated system is a lipid bilayer of lipid+cholesterol simulated 
with coulombtype=PME. I have calculated the energy terms corresponding 
to Coul-SR and LJ-SR as a measure of the electrostatic and van der Waals 
interactions. However after reading some literature and posts I have a 
couple of questions I have not been able to clarify.

1. Is the lipid-lipid term referred only to intermolecular interactions 
or does it include intramoleculars?

2. It seems to me that these energy values in kJ/mol are too large. Are 
they correct or should I do any further calculation or correction (eg. 
number of molecules...)?

Here it is an output of some energy terms form gmx energy (after mdrun 
rerun with the corresponding energy groups):

Energy                      Average   Err.Est.       RMSD Tot-Drift

Coul-SR:Lipid-Lipid      -132802         27    241.483 170.225 (kJ/mol)
Coul-SR:CHOL-Lipid    -1902.18         16    126.736   -19.2265 (kJ/mol)

Any help will be appreciated

Jose A. Teruel

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