[gmx-developers] pdb2gmx default water model

[Thomas Piggot]

I agree. This seems like very a sensible compromise to me.

Tom

Justin A. Lemkul wrote:
> Maybe there should be a hybrid approach from everything that's been said.  Since 
> even the use of SPC/e may be complicated depending on the user's purpose, I 
> don't think there is any true way to make pdb2gmx incredibly smart.  I would 
> vote for providing a default water model for each force field (which is already 
> in place for Encad, anyway), but also always print a big, bold note (much like 
> what grompp does) at the very end of the pdb2gmx output saying that a choice has 
> been made and that this may or may not be suitable for the user's purpose.  I 
> don't see a way to satisfy everyone.  If I choose Gromos96 53A6 for a protein, I 
> may want SPC/e, but if that protein is in a membrane, I want SPC.  There's no 
> way for pdb2gmx to outsmart the user, nor should it try :)
> 
> GROMACS can only do so much to help the learning curve, but I do agree with 
> Michael's assessment that one needs to do some homework before plowing ahead 
> with eyes shut and fingers crossed :)
> 
> -Justin
> 
> Thomas Piggot wrote:
>> 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.