[gmx-developers] pdb2gmx default water model

[Shirts, Michael (mrs5pt)]

I think this is pretty much covers all the bases.  I approve.

Best,
~~~~~~~~~~~~
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>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Thu, 17 Jun 2010 04:01:58 -0400
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] pdb2gmx default water model
> 
> Hi,
> 
> Thanks for the large response on this topic.
> I know this is a delicate issue.
> 
> I realized my initial proposition of spc/e as a default is not a good idea.
> For my own purposes this is usually the best choice, especially because
> of the dielectric constant, but for others the trade-offs will be different.
> 
> Strictly using the water model used to parametrize the force field is also
> not a good idea. CHARMM uses tip3p with LJ on the hydrogen which is
> twice as slow in Gromacs, but also has even less structure than the already
> very understructured tip3p model.
> 
> I am currently leaning towards always presenting the user with a list of
> choices,
> of which the first model is the one we recommend, with "recommended" on
> the line.
> I would then recommend spc for Gromos, tip4p for OPLS and standard tip3p
> for Charmm and Amber.
> That way the user at least realizes that there is a choice to make and
> might look
> more in the issue or simply pick the recommended model which is (in most
> cases)
> not a bad choice.
> 
> Berk
> 
> 
> Thomas Piggot wrote:
>> 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.
>>>>> 
>>>>> 
>>> 
>> 
> 
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