Hi,
On May 2, 2006, at 9:48 AM, David van der Spoel wrote:
gil claudio wrote:
I just derived the conversion of the dihedral
constants from OPLSAA to RB and I get a set of
equations different from the ones printed in the
manual (3.3, p 56).
C1 = V1 / 2 - 3 V3 / 2
C3 = 2 V3
These are the negative of what is printed in the
manual.
I think you're right. Question now is what was used in the
derivation of the parameters? Erik, can you comment?
The equations in the manual are correct, although I did rederive
everything from scratch during the first port.
I bet both of you are forgetting the conversion between polymer and
biochemistry convention. That will give you a minus sign for all odd
powers of cos(phi).
Also the reference (60) is incorrect, it should be
Jorgensen, J. Phys. Chem. 90 (1986) 1276
Finally, do also note that in the latest OPLS paper
Jorgensen & Tirado-Rives J. Comp. Chem. 26 (2005) 1689
a further term is introduced in the torsion function. This is not
yet used in GROMACS AFAIK.
It was present already in the 2001 OPLS-AA/L paper, and we do use it,
although only for a handful of torsions.
The 2005 paper is only a summary/presentation of MCPRO and BOSS as
far as I know - no new data for the force field.
Cheers,
Erik
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