[gmx-users] Re: WCA and free energy calculations

[David Mobley]

Berk,

> Nearly anything can be done now in Gromacs :) (although sometimes not
> easily).
>
> Maybe I missed something, but according to me it should work.
>
> Tabulated potentials work just like any other potential.
> So they are soft-cored when the LJ-parameters or charge of one of
> the two atoms in the pair interaction is different in state A and B.
> So if you have the WCA potential set up propely (maybe using
> energygrp-tables
> if you want different sigma's), then the free-energy part is trivial.

OK, so you're saying that the radii used when looking up interactions
in the interaction table are the "effective radii" including the soft
core modifications? (If not, how can one specify different potentials
to use depending on whether the particle is soft core or not?)

If it's the effective radius -- can I suggest this be documented in the manual?

Thanks for the help. I'd love to be able to do these (have a huge
project planned where this would be immensely useful).

Thanks again,
David


> Berk.
>
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