[gmx-users] Solvation Free energy Calculation

David Mobley dmobley at gmail.com
Thu Oct 19 13:51:29 CEST 2006


> As for the LJ decoupling,I cannot obtain a smooth curve and dG/dlambda
> has large deviations even if I use sc_alpha = 0.5 and sc_power = 1 as
> suggested by Shirts.

This doesn't typically give a smooth curve in the sense of
featureless, like the electrostatics curve. However, the particular
choice of parameters from Shirts typically leads to a smoother curve
than you can get with any other choice of parameters, hence it's the
way to go. I typically end up using a  lot more lambda values for the
LJ curve than the electrostatics for the same reason (16 versus 5), as
you obviously need to put lambda values closer together anytime
dG/dlambda changes rapidly, at least for TI.

Hope that helps.

> I use OPLS-AA forcefield
> I think that there is probably something that I am missing but i don't
> know what.
> Paolo
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