[gmx-developers] Coming on to help in GROMACS development

Berk Hess hessb at mpip-mainz.mpg.de
Thu Mar 10 09:00:29 CET 2005

>Based on my previous research, I've got a few other things that I'll
>be working on that I'd like to put into the next couple releases of
>GROMACS.  Please comment on any of these features that you find
>interesting (or think that really don't need to be implemented, etc).
>1) Improved free energy features, including  
>     a) decoupling free energies capabilities (there are  
>         problems with decoupling energies with Coluomb in 
>         GROMACS currently) 
What do you mean with decoupling?
I have recently implemented free-energy support for Ewald and PME.
Also I have added reaction-field corrections for the exclusions,
with makes free-energy completey correct with RF.

>     b) output suitible for after the fact FEP and Bennett
>     acceptance ratio computations, over multiple states
>     c) an improved, more comprehensive tutorial for free
>     energy calculations.
>     d) including forces from restraints in free energy
>     computations
What kind of restraints?
Position restraints now also support free-energy?


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