On 4/29/18 5:48 PM, Eric Smoll wrote:
Mark,
*Thank you for the reply! *
I understand your conclusion but I am trying to rule out workflow errors on
my part before I make decisions based on the suitability of this
forcefield. Let's say I am testing a QM-geometry optimized molecule with
two identical (same parameters) and coupled dihedrals: phiA and phiB.
Across a QM dihedral relaxed surface scan (RSS), phiA is held at the
initial QM geometry optimized value and phiB is incremented across the 360
degrees of its rotation.
Thus, each step of the QM RSS has two dihedral restraints.
Then, each step of the associated MM RSS should use the same two dihedral
restraints relaxing all other DOF's. The results can be used to calculate a
"restrained" MM PES for phiB.
In this example, how should the "unrestrained" PES be computed with "mdrun
-rerun"? Should both dihedral restraints be removed across each step of the
MM PES scan? Or should the dihedral restrain on phiA stay?
What you need to demonstrate is that the potential energy of the
configuration using the MM energy is equivalent to that of the QM
calculation. That requires the removal of all restraints/biases when
evaluating the energy.
-Justin
"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."
I see. I did not make that connection. Thank you.
Best,
Eric
On Sun, Apr 29, 2018 at 3:13 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:
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
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