[gmx-users] Choosing a f.f. biopolymer system & WFG B3 methanol model

[Christoph Freudenberger]

Nuno R. L. Ferreira wrote:
> In the GROMACS f.f. topologies (molecules) homepage, there's the B3
> three-site methanol model (parameters proposed by van Gunsteren) posted by
> Christoph Freudenberger. Can I use it under gmx and gromos forcefields just
> like that? 
IIRC the model was developed by van Gunsteren to be used in combination
with the gromos FF. Check the reference at the tail of the itp about that.
By heart I don't see any problems about that.

> Nothing to be changed in the function values (constraints field)?
No, it is a rigid solvent model and it should even work with lincs.

> I prepared a system with a peptide and this B3 model.  grompp says that is
> overiding OMET and CMET atomtypes . Because the same atomtypes exist in the
> ff...rtp file, right?
Right.
I implemted the model to be used with the ffgmx, so consistency in atomtypes
was just checked to that model.
But if your not having any other atoms in your protein or lipids using the
same type, you can simply ignore that.

> For a quick inspection, here's the B3 model:
[...]
> ;Model "B3" from W.F. van Gunsteren et.al., JCP 112, 2000, 10450
The name B3 is taken from that paper. Check it for details
about the performance of the model.

regards
-- 
Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785