Dear collegues, I am trying to write an energy function for my molecule that will imitate the results of the amber energy function. For this reason, I calculated all energy terms for my molecule (printed all terms for the 0-th step in energy minimization). However, I find a problem in the very first formula: a harmonic potential for bond stretching. I get the results twice as large as gromacs. I use amber potential. The force constants are of magnitude ~250 000.0 I apply the formula k/2 (b - b0)^2. Amber99 force field. Where can the problem come from?
My molecular system is a molecule of 57 atoms, in vacuum. Best, Dmitrii -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
