Dear gmx-users I am trying to calculate dihedral force constants from the diagonal elements in the hessian matrix in internal coordinates. The matrix is given in hartree/rad^2. Upon conversion to kJ/(mol*rad^2) the values seem an order of magnitude higher than I have seen in the force fields (~3.77 kJ/mol for CCCH dihedral but I get ~42 kJ/(mol*rad^2). The conversion I have used is 2625.5 kJ/(mol*hartree) but is there any consideration needed for the angular units? Another thought I had was, The GROMACS dihedral Potential Energy function #1 (eq 4.62) listed in the manual 4.5.4 is Vd=k(1+Cos(nx-x0)) where x is dihedral angle. so the curvature of this function (second derivative) at the minimum is (n^2)*k so do I need to convert my force constants to this function by k_harm /n^2 = k ?
Any Help would be greatly appreciated Cody Covington -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
