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

Hannes Loeffler Hannes.Loeffler at stfc.ac.uk
Tue May 19 18:00:16 CEST 2015

On Tue, 19 May 2015 17:48:17 +0200
Julian Zachmann <FrankJulian.Zachmann at uab.cat> wrote:

> 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.

That's not what I meant.  I was wondering why you define a, say, ic3
type and an mc3 type.  They are identical!  The charges are explicitly
listed for both states so I think the atom types only affect the vdW


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