[gmx-developers] pdb2gmx default water model

[Berk Hess]

Berk Hess wrote:
> 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...
>   
Ah, in oplsaa the hydrogen database takes care of this.
Except that the atom names and residue names in the output gro do not match
those the tip4p.itp file...

Berk