[gmx-developers] pdb2gmx default water model

[Berk Hess]

David van der Spoel wrote:
> On 6/17/10 10:01 AM, Berk Hess wrote:
>> Hi,
>>
>> Thanks for the large response on this topic.
>> I know this is a delicate issue.
>>
>> I realized my initial proposition of spc/e as a default is not a good
>> idea.
>> For my own purposes this is usually the best choice, especially because
>> of the dielectric constant, but for others the trade-offs will be
>> different.
>>
>> Strictly using the water model used to parametrize the force field is
>> also
>> not a good idea. CHARMM uses tip3p with LJ on the hydrogen which is
>> twice as slow in Gromacs, but also has even less structure than the
>> already
>> very understructured tip3p model.
>>
>> I am currently leaning towards always presenting the user with a list of
>> choices,
>> of which the first model is the one we recommend, with "recommended" on
>> the line.
>> I would then recommend spc for Gromos, tip4p for OPLS and standard tip3p
>> for Charmm and Amber.
>> That way the user at least realizes that there is a choice to make and
>> might look
>> more in the issue or simply pick the recommended model which is (in most
>> cases)
>> not a bad choice.
>
> As long as one can do this non-interactively by a command line option
> as well I agree that this seems to be the best way.
>
The -water command line option now is:
-water       enum   select  Water model to use: select, none, spc, spce,
                            tip3p, tip4p or tip5p

But I just found out there is another issue.
If you select a more than 3-point water model, pdb2gmx changes the water
residue name
and expects more than 3 atoms in the input.
If there are only 1 or 3 atoms in the input, pdb2gmx could simply copy
the oxygen coordinates
as virtual site coordinates.
This would require some programming...

Berk


Berk