[gmx-users] Problem with free energy calculation

Justin MacCallum jlmaccal at ucalgary.ca
Wed Jun 26 19:33:12 CEST 2002

Hi Oliver,

I have been doing a whole series of series of TI calculations using
OPLS/AA and have been getting pretty good results. I get a value of +9.3
kJ/mol which compares favourable with the experimental value. I think part
of your problem may be your choice of temperature coupling options.  At
the very least I think that you should couple the temperature of methane
and water seperately.  If you don't the methane molecule may develop a
very high kinetic energy as it becomes uncoupled from the rest of the
system. A better alternative for flexible multi-atom molecules is to use a
stochastic dynamics integrator which will do a better job at ensuring
energy is partitioned properly within the molecule.  Take a look at Villa
and Mark for more details.

If that doesn't help, there may be something wrong with your topology (I
didn't look that closely), or the model of methane you are using may
simply do a poor job of reproducing hydration free energies.


 > Hi all,
> i=B4m trying an free energy calculation of the solvation energy for one
> methane molecule in a box of water.
> I have made 20 simulations for different values of lambda from 0 to 1
> and integrated the resulting free energy, but the energy is far too
> large. I got a solvation energy of nearly 30 kJ/mol.!!
> I have attached my files to this mail and hope that someone can help
> with my problem.

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