[gmx-developers] pdb2gmx default water model

[Shirts, Michael (mrs5pt)]

> I thought about that, but I think that choice is asking too much in
> terms of knowlegde
> from the general user.

See, I'm all in favor of making them think a little.  If you don't know what
water model you should use, you don't deserve to be running a simulation.

Make them look up what they should be running, as long as the error message
pretty clearly says that - something like:

"Please investigate which water model is most appropriate for the force
fields you are using.  SPC/E has the best overall properties for pure water,
but may not be optimally compatible with all force fields.  Gromacs tries to
make running your simulations better, faster, and easier, but cannot always
tell you what simulation you should be running!"

(I'd argue TIP4P-Ew properties are about as good as SPC/E, but your call on
that!).

~~~~~~~~~~~~
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434)-243-1821


> From: Berk Hess <hess at cbr.su.se>
> Date: Wed, 16 Jun 2010 11:13:11 -0400
> To: "michael.shirts at virginia.edu" <michael.shirts at virginia.edu>, Discussion
> list for GROMACS development <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] pdb2gmx default water model
> 
> 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
>