[gmx-users] FEP and error estimation

Tomas Kubar tomas.kubar at uochb.cas.cz
Tue Jan 24 10:48:34 CET 2006


1. The RCA analysis is implemented as a method of free-energy 
calculation inside mdrun (free-energy=yes & 
free-energy-method={something}, so no script is needed). For the user's 
convenience, only a few extra keywords in the mdp file are used to 
control the RCA run.
2. I've put it into our local version, making use of the constructions 
that are present in the 3.3 itself. I'm afraid I don't have a concise 
documentation but the changes are commented in the source (in an easily 
comprehensible way, I hope :-) and there is a summary of all changes made.

I can send the modified source to you if you wish.


Alexandre Suman de Araujo wrote:

> I ´ll read the paper that you pointed but it looks like interesting.
> Did you implemented the technique as compiled program or as a script?
> I´m very interested in minimize errors in TI method.

I've seen the paper and had been wanting to try playing around with it

a bit on my test system. Is it in 3.3 itself already, or do you mean
you've put it into your local version of 3.3? In either case, I'd be
interested in trying it out if you can provide documentation.


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