[gmx-users] ffgmx: CH2-CH2 Dihedral

[Dallas Warren]

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?

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy
Monash University
381 Royal Parade
Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9076
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