Hi Francois,
Thank you for your help. I am reading these two articles and they are very good. I am going to run two systems, one using GAFF for both solute and solvent and the other one using GAFF for the solute and OPLS for the solvent. Then I can test both systems and decide which one to use in the production run.
Thanks,
Guoxiong
On Feb 22, 2012, at 2:12 AM, FyD wrote:
> Thomas, Guoxiong,
>
> About mixing force fields, see:
>
> - The Gromacs page .
> http://www.gromacs.org/Documentation/How-tos/Parameterization :
>
> "You should not mix and match force fields. Force fields are (at best)
> designed to be self-consistent, and will not typically work well with
> other force fields. If you simulate part of your system with one force
> field and another part with a different force field which is not
> parameterized with the first force field in mind, your results will
> probably be questionable, and hopefully reviewers will be concerned.
> Pick a force field. Use that force field.
> If you need to develop new parameters, derive them in a manner
> consistent with how the rest of the force field was originally
> derived, which means that you will need to review the original
> literature. There isn't a single right way to derive force field
> parameters; what you need is to derive parameters that are consistent
> with the rest of the force field. How you go about doing this depends
> on which force field you want to use. For example, with AMBER force
> fields, deriving parameters for a non-standard amino acid would
> probably involve doing a number of different quantum calculations,
> while deriving GROMOS or OPLS parameters might involve more (a)
> fitting various fluid and liquid-state properties, and (b) adjusting
> parameters based on experience/chemical intuition/analogy...."
>
> - Then O. Guvench & A. D. MacKerell, in Molecular Modeling of
> Proteins, ed. K. Andreas, Humana Press, Totowa, NJ, 2008, vol. 443, p.
> 63.
>
> We also discussed this topic in the context of Amber vs GLYCAM and
> Amber & GLYCAM:
> http://pubs.rsc.org/en/content/articlelanding/2011/cp/c1cp20854c
>
> regards, Francois
>
>
>> I meant the same as Francois, mixing two force fields is dangerous.
>> Better to stick with one. The problem is the interaction between both
>> force fields, think nobody investigated how they should interact. So if
>> you find a way for doing this and want to publish your results you must
>> convince the reviewer of the journal that your way has absolute no flaws.
>> If you accomplish this, and can convince many people, than i think you
>> can hope for many citations (because it is now accepted that one can mix
>> both force fields). But this would need very much work.
>> So the easier way is to use one force field and stick with it, since you
>> want to investigate your system. And not how to mix two force fields
>> (much more work then only to investigate your system).
>>
>>
>>
>> Am 21.02.2012 17:55, schrieb Guoxiong Su:
>>> Dear Francois,
>>>
>>> Thank you for your reply. I will do as suggested to find a RESP
>>> charge for OPLS.
>>> Then how can I get the LJ parameters between those 'GAFF-particles'
>>> and 'OPLS-particles' since they are using two kinds of combine
>>> rules?
>>>
>>> Sincerely,
>>> Guoxiong
>>>
>>> On Feb 21, 2012, at 10:27 AM, FyD wrote:
>>>
>>>> Dear Guoxiong Su,
>>>>
>>>> Mixing two force fields is always dangerous.
>>>>
>>>> I would compute a highly consistent set of charges for all the
>>>> molecules to be studied. If you want to use OPLS you can find a RESP
>>>> approach for OPLS.
>>>> See R. H. Henchman and J. W. Essex, J. Comput. Chem., 1999, 20, 483?498.
>>>> This approach should be easy to implement in the R.E.D. program.
>>>>
>>>> A new box for benzonitrile can be created for Amber.... Then, whatever
>>>> you decide to use (may be try first SCNB = 2.0& SCEE = 1.2) your
>>>> benzonitrile box has to be tested/studied...
>>>>
>>>> regards, Francois
>>>>
>>>>
>>>>> I am trying to solvate a molecular triad in a benzonitrile box. For
>>>>> this molecular triad, I used Antechamber to generate the topology
>>>>> file with GAFF. The charge is calculated using AM1-BCC. I have done
>>>>> some literature search and I found OPLS force filed has the
>>>>> parameters for benzonitrile. Is it reasonable to mix GAFF with OPLS
>>>>> force field in AMBER?
>>>>>
>>>>> I have read though the mailing list and I found some people was
>>>>> mixing AMBER force field with the Glycam force field (e.g.
>>>>> http://archive.ambermd.org/200906/0240.html). I knew that for GAFF,
>>>>> SCNB = 2.0 and SCEE = 1.2. What values are they in OPLS? Is it 1.0
>>>>> since OPLS doesn't have any scaling? The combine rules of GAFF and
>>>>> OPLS for the Lennard-Jones potentials are different as well. GAFF
>>>>> follows the AMBER rules and OPLS uses geometric mean for sigma and
>>>>> epsilon. Is it possible to use two kinds of combine rules in AMBER?
>
>
>
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Received on Wed Feb 22 2012 - 12:30:02 PST
