[gmx-users] Re: Free energy blowing up

David spoel at xray.bmc.uu.se
Fri Nov 11 22:59:22 CET 2005

On Fri, 2005-11-11 at 16:53 -0500, Michael Shirts wrote:
> If you are mutating one atom A->B, there is no need to use soft core,
> as there is no problem with singularities.  Actually, it would
> probably make things worse.  I'd stick with linear interpolation in
> the A and C parameters (i.e., where U(r) = A/r^6-C/r^12 -- this will
> likely work better than linear interpolation in epsilon and sigma, as
> the "core" that is excluding water will change less rapidly.

In principle correct but H usually does not have LJ, so he is growing a
LJ particle here. In that case Soft-core is needed.

> Also, with a change like this, I would highly suggest not using a slow
> growth type simulation.  As has been pointed out, hysteresis is not
> your friend.  Instead, run a number of equilibrium simulations at
> intermediate with no change in lambda.  Collect the average <dH/dL>,
> and numerically integrate.  Changing A->B, the curve should be fairly
> smooth, allowing for higher order integration techniques, and fewer
> points.  I bet 5-10 will be sufficient.
> Best,
> Michael Shirts
> Research Fellow
> Columbia University
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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