[gmx-developers] pdb2gmx default water model

[Berk Hess]

Berk Hess wrote:
> 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
>
>   
I committed the water model selection code and water model list files
described above.

Currently pdb2gmx with tip4p or tip5p with water in the pdb file only
add vsites for oplsaa
and then with incompatible atom and residue names.
I don't feel like putting more effort into this now.

Berk