[gmx-developers] pdb2gmx default water model

[Thomas Piggot]

Maybe I am wrong but I thought that different water models are more (or 
less) appropriate for certain systems, as well as being forcefield 
dependant?

For example SPC has been shown to perform better than SPC/e when 
simulating membranes (Tieleman and Berendsen 1996 J Chem Phys) but SPC/e 
is better than SPC when simulating proteins (Hess and van der Vegt 2006 
J Phys Chem B). Doesn't this make things more complex than having a 
single appropriate default model for a forcefield?

And also what about the issues where it is not so clear as to which 
model is the appropriate default. For example CHARMM TIP3P Vs. standard 
TIP3P model for use with the CHARMM forcefield. Would it be standard 
TIP3P because of the increase in speed as discussed in the recent 
ffcharmm paper or would the more commonly used CHARMM TIP3P be a better 
choice?

Because of these points I think having SCP/e as default with a clear 
message saying that the user should be warned that this may not be the 
best water model for their system would be the best way to handle this.

Cheers

Tom

Anton Feenstra wrote:
> On 16/06/10 17:24, Shirts, Michael (mrs5pt) wrote:
>>> 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:
> [...]
> 
> I don't agree here. Yes, the user should be responsible for her choices, 
> but also a good tool should come with a *full* set of appropriate 
> default options. Then, it is clearly the responsibility of the user to 
> assert their validity for a particular application.
> 
> Is/are there (a) paper(s) that say that either SPC or SPC/e is the 
> better water model? If most non-expert users would prefer SPC /or/ most 
> reviewers would require that (for historical reasons of no other /or/ 
> some well-cited papers highlight SPC as the best option, then I'd argue 
> to leave that the default.
> 
> Expert user will (want to) know better ;-)
> 
> B.t.w., how transferable are water models between ff's? I've always been 
> thought that they are actually non-transferable (or at least that is 
> what I remember), making e.g. Amber/SPCe a bad option, as would 
> gromos/tip4p.
> 
> 

-- 
Dr Thomas Piggot
University of Southampton, UK.