[gmx-users] Alkane dihedral from OPLS to Ryckaert-Bellemans

[Sung Hyun Park]

Hi,

I'm a gromacs beginner and have a quick question.

My system includes a simple n-decane molecule with oplsaa force field. I'm basically confused with
the Ryckaert-Bellemans parameters in ffoplsaabon.itp file in gromacs for H-C-C-H alkane dihedral.

The OPLSAA parameters for H-C-C-H dihedral for alkane is given as (in kcal/mol):
(W. L. Jorgensen et al. J. Am. Chem. Soc. 118, 11225 (1996))

V1 = 0
V2 = 0
V3 = 0.318
V4 = 0

According to the gromacs manual, the OPLSAA parameters are translated to Ryckaert-Bellemans
parameters in the following way:

C0 = V0+V2+(V1+V3)/2
C1 = (3*V3-V1)/2
C2 = -V2 + 4*V4
C3 = -2*V3
C4 = -4*V4

So the translated Rykaert-Bellemans parameters are (kJ/mol): 

C0 = 0.66526
C1 = 1.99577
C2 = 0.00000
C3 =-2.66102
C4 = 0.00000

In the ffoplsaabon.itp files in gromacs, I find the only dihedral that matches these numbers  in
Rykaert-Bellemans parameters is the following:

HC CM CT HC 3 0.66525  1.99576  0.00000  -2.66102  0.00000  0.00000 ; alkene     

I am not sure if this is the correct one to use because it says "alkene". And it lists "CM" as the
second atom, not the usual "CT". What does "CM" stand for? If this is not the correct choice, what
is the correct one to choose in ffoplsaabon.itp for the simple H-C-C-H dihedral for n-alkane molecules?

I appreciate your kind help in advance.

Regards,
Sung Hyun