[gmx-developers] pdb2gmx default water model

[Michel Cuendet]

Hi,

I think the default water model should be the one with which the force
field has been parametrized. The water is an integral part of the force
field. It would be hard to justify changing it for a typical protein
simulation.

What we did for the charmm force field, is that the user can choose
between two flavors of TIP3P, as indicated in the forcefield.itp file :

#define _FF_CHARMM
; The user has the choice between:
;     - Original TIP3P model [Jorgensen et al. J Chem Phys, 1983] ,
which uses
;     the fast gromacs optimizations
;     - CHARMM TIP3P [MacKerell et al. J Phys Chem B, 1998] with LJ
interaction
;     sites on the hydrogens, about 2 times slower
; The original model is used by default, to use the CHARMM version
include in
; your mdp file :
;     -DCHARMM_TIP3P

The water model could also be determined via environment variables set
in the forcefield.itp file. It could then be changed by the user with a
-D flag in the mdp file.

Best,
Michel


On 06/16/2010 11:26 AM, gmx-developers-request at gromacs.org wrote:
> Hi,
>
> pdb2gmx currently has spc as the default water model.
> But now I have ported the Amber force fields to Gromacs, I don't want to
> add the spc model
> to Amber and spc is a bad model anyhow (although tip3p is even slightly
> worse).
> The question is what to do.
> I see two options:
> 1) make spc/e default, which is better than both spc and tip3p
> 2) make the default water model force field dependent, this requires
> an extension of one of the pdb2gmx input file formats and some coding in
> pdb2gmx
>
> What are your preferences or suggestions?
>
> Berk
>
> ==========================================================
> Michel A. Cuendet, Ph.D
> Department of Chemistry
> New York University
> 100 Washington Sq. East
> New York, NY 10003
> http://lausanne.isb-sib.ch/~mcuendet/ 
> ==========================================================
>
>