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 - 00:30:01 PST
