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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
