[gmx-developers] pdb2gmx default water model

[Shirts, Michael (mrs5pt)]

Hi, all-

> I don't agree here. Yes, the user should be responsible for her choices,
> but also a good tool should come with a *full* set of appropriate
> default options. Then, it is clearly the responsibility of the user to
> assert their validity for a particular application.

BUT- a good tool should also make sure the user is aware that there is a
choice to be made.  So forcing an option with a default option i.e. There's
some option -water with -water ffdefault being one option (gives the default
for the ff selected) -- but -water being a required option.  If you don't
include it you get a warning to include it, saying that --ffdefault will
give the default for the force field (and list the defaults for each force
field).
 
> Is/are there (a) paper(s) that say that either SPC or SPC/e is the
> better water model?

There's a paper that shows that TIP4P-Ew is a better bulk model than the
other TIPXX models from about 10 to 100 C.
(H. W. Horn, W. C. Swope, J. W. Pitera, J. D. Madura, T. J. Dick, G. L.
Hura, and T. Head-Gordon. Development of an improved four-site water model
for biomolecular simulations: TIP4P-Ew. J. Chem. Phys. 2004, 120, 9665-9678.
doi:10.1063/1.1683075)

There is presumably such a paper for SPC/E as well.

> If most non-expert users would prefer SPC /or/ most
> reviewers would require that (for historical reasons of no other /or/
> some well-cited papers highlight SPC as the best option, then I'd argue
> to leave that the default.

Amber, charmm and OPLS-AA were developed with TIP3P, and that should be the
default.  Except that charmm uses a TIP3P with lennard-Jones on the waters,
and that should probably be the default with charmm.
 
> B.t.w., how transferable are water models between ff's? I've always been
> thought that they are actually non-transferable (or at least that is
> what I remember), making e.g. Amber/SPCe a bad option, as would
> gromos/tip4p.

Nobody really knows.  But it's unlikely to help.  I have a paper with
solvation free energies of OPLS-AA side chain analogs with a bunch of water
models: doi:10.1063/1.1877132. TIP3P is the best, though others aren't that
much worse.

But there is no general answer.