[gmx-developers] doing energy evaluations at alternate lambda values (i.e. for bennett acceptance ratio)

David Mobley dmobley at gmail.com
Fri Jan 5 16:01:44 CET 2007


> PME can be handled in two different ways. If it's a matter of
> decoupling, Berk has implemented a pretty smart hack where grompp can
> exclude all nonbonded interactions between two arbitrary groups, and
> then add them back as listed interactions (think faked 1,4) so all of
> them are included.

Right. I was involved with cooking up this scheme, as it's something
I'm currently using for LJ interactions by manually editing the pairs
and nonbonded interactions, although I haven't used Berk's
implementation for electrostatics yet.

> The advantage of this approach is that you get rid of the lattice
> complications where a decoupled molecule is interacting with the
> periodic copies of itself, and since the decoupled interactions are
> listed explicitly we can forget about the PME part too.

Right. Up to this point I don't do electrostatic decoupling as I'm
still using 3.3 (for continuity reasons I don't like to switch
versions mid-project), but presumably I'll go that direction in the
future, so this is an option.

> Alternatively, we have the group-based PME approach (that was
> complicating my code :-). This is going to be slightly more
> expensive, but probably not more than 5-10% of runtime. Once we have
> the separate group contributions we can calculate the potential for
> as many lambda points as you want without extra cost.

Ahh. That sound intriguing.

Keep me posted -- as soon as you have this ability to do multiple
lambda values in I'm happy to help with testing.


> Cheers,
> Erik
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