[gmx-developers] pdb2gmx default water model

[Berk Hess]

Shirts, Michael (mrs5pt) wrote:
>> 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?
>>     
>
> I'd vote for 2) -- make the default water model dependent on the force
> field.  But is there an option 3, where the user is required to specify the
> water model they want to use?
>
>   
I thought about that, but I think that choice is asking too much in
terms of knowlegde
from the general user.

I'd personally always choose for spc/e, but referees and therefore users
might be less happy
with that.
On the other hand most properties, except for the dielectric constant,
are not affected
significantly by the water model.

This means someone (I'm afraid that's going to be me) has to add a water
model field
to, I guess, the rtp files.

Berk