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

[David Mobley]

Erik,

I'm happy to help with testing. Shoot me an e-mail when you think
you've got it working properly and let me know how to get the code
with these modifications. An array of lambda values sounds more or
less like how I was thinking to do it, although I was also planning to
add a flag to only bother doing the extra energy evaluations every
(nstlambda) steps or some such.  More to follow.

Thanks,
David


On 1/4/07, Erik Lindahl <lindahl at cbr.su.se> wrote:
> Hi David,
>
> I actually have _most_ of this working; the remaining part is to
> correctly propagate an array of lambda values into all different
> places like bond constraints, pulling, etc., but I was stupid enough
> to do it in the same tree where I implemented group-based PME, so
> some things got a bit complicated, and then I was just too busy in
> november/december :-)
>
> Friday is a holiday here, but if you'd be willing to help with
> testing I can probably try to copy just the lambda modifications into
> a fresh tree early next week.
>
> Cheers,
>
> Erik
>
>
>
> On Jan 4, 2007, at 12:37 AM, David Mobley wrote:
>
> > Dear all,
> >
> > We're attempting to modify mdrun to be able to write out the system
> > total potential energy evaluated at a number of alternate lambda
> > values during a free energy calculation, when energies are written to
> > output. (The goal is to use this output for doing free energy
> > calculations with Bennett Acceptance Ratio or other methods which
> > require potential energies evaluated at a variety of alternate lambda
> > values).
> >
> > I'm assuming this would be a straightforward (perhaps 20 minutes?)
> > task for anyone who already knows the inner workings of the code, but
> > since I'm not that familiar with it, it seems a bit more difficult for
> > me. Is there anyone who wants to volunteer?
> >
> > If not, can anyone help by telling me the complete set of function
> > calls that need to be done in the inner loop of do_md(), in order to
> > safely:
> > 1) Change the current lambda value to some other lambda'
> > 2) Compute the new total energy
> > 3) Restore lambda to its original value so the simulation can
> > continue.
> >
> > Thanks very much in advance.
> >
> > Sincerely,
> > David Mobley
> > UCSF
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