[gmx-developers] pdb2gmx default water model

[Anton Feenstra]

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.


-- 
Groetjes,

Anton
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|  _   _  ___,| K. Anton Feenstra                                     |
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