Hi, This question is a sequel of sorts to my earlier question about dihedral parameters in Gromacs (http://lists.gromacs.org/pipermail/gmx-users/2012-October/075860.html).
I typically use the OPLS-AA force field. In OPLS-AA, dihedrals are usually specified with the Ryckaert-Bellemans function. In Table 5.5 on page 125 of Section 5.7 of the manual, such a Ryckaert-Bellemans function specification is called a type 3 dihedral. This is why there is a 3 in the function type column in the dihedral section of the OPLS-AA ffbonded.itp file. One can also use type 1 dihedrals, which, as shown in the manual, have the simple potential energy form V_d(phi_ijkl) = k_phi (1 + cos(n*phi - phi_s)). However, in the CHARMM force field ffbonded.itp file included in Gromacs, it seems that all of the [ dihedraltypes ] are specified using dihedral function type 9. Here is an example from the CHARMM ffbonded.itp: ; i j k l func phi0 cp mult C CT1 NH1 C 9 180.00 0.8368 1 If you have time, I have two questions about type 9 dihedral functions: (1) What is a type 9 dihedral? On page 74 of Section 4.2.12 of the manual, it says, "For certain force fields, type 9 is useful. Type 9 allows multiple potential functions to be applied automatically to a single dihedral in the [ dihedral ] section when multiple parameters are defined for the same atomtypes in the [ dihedraltypes ] section." What does this mean? What does it mean to apply multiple potential functions to a single dihedral? Is this a fundamentally different way of specifying a dihedral? (2) In that above example from the CHARMM ffbonded.itp, what is the "cp" column? Table 5.5 of on page 125 of Section 5.7 of the manual seems to say that in type 9, phi_s, k_phi, and the multiplicity are specified. Does this mean that "cp" corresponds to the force constant k_phi? Thank you for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
