[gmx-users] Fwd: Bad performance in free energy calulations

Julian Zachmann FrankJulian.Zachmann at uab.cat
Tue May 19 17:48:20 CEST 2015

Hello Hannes,

As Michael said it is better to leave most things untouched and just change
VDW and LJ - at least this is what I have been reading so far.

Concerning the changes of the atom types: the changes in the charges are
really small and the results will probably be the same if I would not
convert the whole ligand, just the 4 atoms which are changing. However, as
i had both ligands parametrised, I thought it would be a good idea to
really convert the whole ligand from one to the other, and change all
charges on all atoms.

Probably it won't really make any difference.

All the best,

2015-05-19 17:37 GMT+02:00 Michael Shirts <mrshirts at gmail.com>:

> >
> > somewhat off-topic but I wonder why in your free energy protocol you
> > only vary the vdW and electrostatic lambdas.  What about the others?
> > Your mutation also transforms bonded terms and masses.
> >
> Minor point - if you are taking the difference between two mutations (say,
> with and without a ligand), then it's better to leave the masses untouched
> -- any contribution will cancel.  There are some weird issues with changing
> masses in the constraint terms and their contribution to the free energies
> that need to be accounted for post-hoc.
> --
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Julian Zachmann
Laboratori de Medicina Computacional
Unitat de Bioestadistica. Facultat de Medicina
Universitat Autonoma de Barcelona
08193 Bellaterra (Barcelona). Spain
Phone: (3493) 581 2797
Fax:   (3493) 581 2344
E-mail: FrankJulian.Zachmann at uab.cat

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