[gmx-users] VdW and Coulomb SR contribution to dVdl in thermodynamic integration

Berk Hess gmx3 at hotmail.com
Mon Apr 14 18:19:13 CEST 2008

I guess you are using soft-core interactions.
In that case there are more terms in dV/dl, see eq. 4.120 in the manual.


> Date: Mon, 14 Apr 2008 18:13:32 +0200
> From: reich at mpikg.mpg.de
> To: gmx-users at gromacs.org
> Subject: [gmx-users] VdW and Coulomb SR contribution to dVdl in thermodynamic integration
> Dear Gromacs-users,
> I have been doing a test thermodynamic integration for the conversion of
> methanol into a dummy molecule in water. I have been interested in the
> contribution of the VdW and Coulomb short range interaction to dVdl.
> According to equations 4.108 and 4.104, at lambda=0 (the methanol-state)
> the contributions should be the negative Lennard-Jones and Coulomb short
> range interaction energies between methanol and the surrounding water. I
> have been calculating the interaction energies with g_energy (choosing
> LJ-SR:methanol-rest and Coul-SR:methanol-rest as options). For example for
> a particular step in my trajectory I get
> -7.954321 kJ/mol for the Lennard-Jones interaction
> and -56.966656 kJ/mol for the Coulomb intercation between methanol and water.
> So the contribution of the combined interactions to dVdl should be
> 64.921 kJ/mol
> I have, however, also used the option sepdvdl with mdrun to get some
> detailed information on dVdl during the simulation.
> The line from the log-file giving me the contribution of Lennard-Jones and
> Coulomb short range interactions for the simulation step in question is:
>   VdW and Coulomb SR particle-p. V -1.49467e+04  dVdl  1.01145e+03
> So the simulation output gives me a result that is two magnitudes greater
> than what I calculated! Is there anything wrong with my reasoning or do
> you have any other clue why I end up with two different results?
> Thanks
> Luther
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