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

[David Mobley]

Erik,

Any progress on this? We'd love to get it working as soon as possible.

Thanks a lot,
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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