[gmx-users] Fwd: Internal energy

[Alex]

Any comment please?

Thanks.


---------- Forwarded message ----------
From: Alex <alexanderwien2k at gmail.com>
Date: Tue, May 9, 2017 at 12:49 AM
Subject: Internal energy
To: gmx-users at gromacs.org


Hi gromacs user,

A peptide(p), a solid surface(s) in water(w) solution are the three
ingredients of my system. The total internal energy (Utot) of the system in
NVT ensemble, can be defined as Utot = Upp + Uww + Upw + Usw + Ups , where
the Uxy is the internal energy of interaction between x and y.
Now my question is that how I can simulate each of these portion in a NVT
ensemble simulation?

I use the "energygrps = peptide surface water" in my mdp file, but my gmx
energy -f case.edr does not contain any of those Uxy, but it has something
like  Coul(LJ)-SR:x-y, Coul(LJ)-14:x-y, I was wondering if the sum over
these Coul(LJ):x-y would give me the Uxy?


Also, is the "Total-Energy" in the gmx energy the total internal energy of
the system Utot which shows up in the Helmholtz  free energy, A = Utot-TS?

Thanks,
Kind regards,
Alex