[gmx-users] Strange dgdl-value together with lincs

David Mobley dmobley at gmail.com
Wed Feb 20 17:38:53 CET 2008


>  Assume, you take the interconversion of ethane to methanol in solvent in
>  one step.
>  You sample hardcore at 11 evenly spaced lambda values for, lets say, 2
>  ns each.
>  You get the dG/dl mean from every run and integrate via simpson to get a
>  total DG.

Hold on, if you are doing this with hardcore, there is a singularity
in dG/dlambda. It won't be numerically integrable so whatever you
compute will be in error. See my recent JCP paper that I referred you
to before.

I think if you are using hardcore, you *have* to use slow growth and
the Jarzynski or Crooks expressions, or do some sort of polynomial fit
to the singularity in dG/dlambda and integrate the polynomial.
Integrating dG/dlambda directly will simply fail since you can't
numerically integrate a singularity.

If you're using softcore, you have more options, and simple numerical
integration can work.

For what it's worth, too, a delta_lambda of 0.02 is insanely fast
"slow growth".


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