[gmx-users] ffgmx: CH2-CH2 Dihedral

[K.A. Feenstra]

Dallas Warren wrote:
> Erik,
> 
>> A lot of MD force fields have this problems with aliphatic dihedrals. 
>> I would guess that OPLS is slightly better than Gromos96, which in 
>> turn should be better than Gromacs. (The "gromacs" force field is 
>> really Gromos87 with some modifications mentioned in the manual - we 
>> don't try to develop our own force field, it is too
>> much religion in it :-)
> 
> 
> I could imagine that, they are not simple things.  And you should be 
> concentrating on making GROMACS faster anyway ;-)
> 
>> If you want to stick to united atom I would recommend either 
>> Ryckaert-Bellemans potentials or The Kuwajima alternative. The R-B 
>> potential is already defined
>> in Gromacs; just change the dihedral type to "3" and make sure you 
>> REMOVE the 1,4 interactions since these are included in this 
>> functional form.
> 
> 
> Sticking with a united atom FF at the moment.  Changed the topology to 
> include the Ruckaert-Bellemans potential for butane and then minimised 
> it.  It is much better :-)  Here are the values FYI:
> 
>                         GROMACS R-B             Allinger et al.
> diff anti/gauche        6.6 kJ/mol      2.9 kJ/mol      2.6 kJ/mol
> 
> Currently have a decane simulation running to see how the relative 
> populations of anti/gauche go.
> 
> What do the protein people use for the various CH2-CH2 dihedrals that 
> are within some of the amino acids when running simulations with the 
> GROMACS force field?  Or is one of the other FF typically used?  From 
> what I can tell, even if there is a single CH2-CH2 dihedral within the 
> amino acid it will be far more rigid than it should be, and hence not 
> show the confirmation dynamics that it should.  Or am I wrong in my 
> thinking here?

I'm one of the protein people, and for all I've heard and read the
Gromos 98 forcefield is at least one of the best. That doesn't mean
there is nothing to improve...



-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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