[gmx-users] Dihedral parameters from QM and MM relaxed surface scans
mark.j.abraham at gmail.com
Sun Apr 29 23:14:00 CEST 2018
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
On Sat, Apr 28, 2018 at 9:30 AM Eric Smoll <ericsmoll at 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"
> 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?
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