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

[Mark Abraham]

Hi,

On Wed, Dec 6, 2017, 3:11 AM Jose <teruel at um.es> wrote:

> 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?
>

It doesn't matter how you define it - the force fields are additive, but
not decomposable in this way.

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...)?
>

They are for all the atoms in the group, so if you want per molecule or per
atom then you have some arithmetic to do.

Mark

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
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.