[gmx-users] thermodynamic integration

David Mobley dmobley at gmail.com
Sun Oct 28 04:46:49 CET 2007


> is it possible to do thermodynamic integration in Gromacs using non-linear scaling of the lamda paramerter?

I'm not sure exactly what you mean, so first I'll answer what I think
you mean, and then tell you what I think you ought to be asking. :)

If you mean, "Is it possible to perform a transformation where H =
(1-lambda)^k*V_0 + lambda^k*V_1, where k is some exponent larger than
1, and V_0 and V_1 are the two potentials in question?" the answer is

If you mean is it possible to use some functional form other than
linear scaling, the answer is yes (soft core potentials are

If you want to know how you *ought* to be doing things, the answer is
that you ought to be doing linear scaling if it's a simple
electrostatics transformation, and using soft core potentials (which
are available in GROMACS) if you're inserting or deleting atoms. You
might see this preprint
which should be out in JCP soon, for some reasons why and references
to other relevant literature.

Best wishes,

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