[gmx-users] Re: Free energy blowing up
dmobley at gmail.com
Fri Nov 11 23:16:22 CET 2005
On 11/11/05, David <spoel at xray.bmc.uu.se> wrote:
> 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.
Yes, I agree with David on this one, unless he's using hydrogens which
already have LJ.
It would be relatively simple to check -- if indeed there are problems he
should see shot-like noise on his dv/dlambda time series absent soft-core,
and the distribution of dv/dlambda should be decidedly non-gaussian. Things
should look much better with soft core. On the other hand, if there are no
problems, both should look OK.
> > 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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