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

[Julian Zachmann]

>
> > 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
> terms.


There is no specific reason for it. After the parametrisation of the
ligands I just took for both of them all atom types and use them for the
ligand conversion - whether they are identical, only slightly different, or
not.


2015-05-19 18:00 GMT+02:00 Hannes Loeffler <Hannes.Loeffler at stfc.ac.uk>:

> 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
> terms.
>
> Cheers,
> Hannes.
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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
http://lmc.uab.es