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

Erik Lindahl lindahl at cbr.su.se
Thu Jan 4 10:20:34 CET 2007

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.



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
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