Hi, Your two PES scans are over the same coordinates, and by construction you are balancing the normal FF contributions against an intended-as-strong restraint. The only thing that is different between your two sets of PE calculation is the contribution of the restraint. If the normal FF was parameterized for the species and configurations of interest, then you'd observe that the unrestrained PES matched the restrained PES, ie that the contributions from the restraint were negligible. Clearly that isn't the case, so the only available conclusion is that the normal FF isn't suitable for modelling this PES. Whether that is a useful conclusion about the chances for quality observations of quantities that depend on the FES is less clear.
Mark On Sat, Apr 28, 2018 at 9:30 AM Eric Smoll <ericsm...@gmail.com> wrote: > 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. > -- 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.
