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

reich at mpikg.mpg.de reich at mpikg.mpg.de
Wed Apr 16 14:55:31 CEST 2008

Oh dear,

yes I do use a soft core potential and I overlooked that I set sc-power to
1. So even at lamda=0 there should be a soft core contribution to dV/dl!

Thanks Berk.

>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
>> 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
>> the contributions should be the negative Lennard-Jones and Coulomb
>> range interaction energies between methanol and the surrounding water.
>> 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
>> 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
>> Coulomb short range interactions for the simulation step in question
>>   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
>> 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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