Hello Gromacs Users, I am trying to reproduce some published forcefield development work. In this paper, dihedral parameters are derived from QM and MM relaxed surface scan data collected on individual small molecules in vacuum.
My replication workflow is as follows. The MM relaxed surface scan trajectory was prepared by concatenating the final frame of a set of energy minimization calculations. Each energy minimization held the dihedral of interest at a desired angle with a 1000 kJ/mol dihedral restraint. Other DOF's were allowed to relax with the "steep" algorithm in single-precision GROMACS 2018.1 to machine precision. A "restrained" dihedral PES was calculated by collecting the molecule's potential as a function of dihedral angle *with the restraint on the dihedral of interest*. An "unrestrained" dihedral PES was also calculated by removing the dihedral restraint on the dihedral of interest and calculating the energy with the rerun feature of mdrun. I find that the "restrained" MM dihedral PES is in excellent quantitative agreement with QM relaxed surface scan data. The "unrestrained" MM dihedral PES is only in qualitative agreement with the QM results. Peaks and dips in the "unrestrained" PES are exaggerated when compared to the "restrained" PES. As far as I understand, the "unrestrained" PES should be more appropriate/accurate than the "restrained" PES. Am I correct? Is there a flaw in my workflow? Best, Eric -- 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 gmx-users-requ...@gromacs.org.