Karl,
Thank you so much for looking into this so thoroughly. I don't honestly
know if the dihedral effect is important. The goal of my work is to
simulate crystallization of acetaminophen form I and form III. For self
assembly of organic molecules, or solid state crystal crystal calculations,
much care is typically paid towards the selection of the partial atomic
charges. However, the dihedral angle importance isn't as clear to me. Do
you have any thoughts here? My experience rests solely in MD, and I am not
familiar with the various levels of DFT theory you are referencing.
Although, the differences between the MD and DFT dihedral energy graphs is
obvious.
Can someone answer how to evaluate the dihedral energies of an angle that
has multiple parameters from the gaff.txt file? I am implementing this in a
group MD code, and want to make sure the procedure is right. I am currently
assuming I just evaluate the dihedral energy for each parameter set, and
sum over the multiple parameter sets.
Regards,
Conor Parks
B.S.E in Chemical Engineering, University of Michigan, 2012
PhD candidate in Chemical Engineering, Purdue University
On Wed, May 4, 2016 at 4:28 AM, Karl Kirschner <k.n.kirschner.gmail.com>
wrote:
> Hello Conor,
>
> I got curious about your molecule and took a look at it. I did some quick
> HF/6-31G(d) calculations and found two minima that were close in energy -
> one that is the conformation you sent out, and a second lower energy (by
> 0.43 kcal/mol) conformation where the amide group functional group is
> rotated 180 degrees (see attached figure that contains the AM1-BCC charges
> for this conformation). I verified that they are minima on the potential
> energy (PE) surface by doing frequency calculations. I also did two sets
> of torsion rotations, one for each functional group of the phenyl ring. I
> then compared how the gaff parameters perform using the AM1-BCC charge set
> (see attached PE figures). The rotation of the hydroxyl group looks decent,
> in my opinion. However, the rotation of the amide functional group deviates
> significantly from the HF/6-31G(d) results. Around both HF/6-31G(d) minima
> (0 and 180 degrees), the molecular mechanics (MM) calculations predict a
> double well potentials.
>
> I would say these are preliminary results. To really verify the QM
> surface is reliable, I would suggest doing the calculations at a more
> rigorous theory level (e.g. MP2/aug-cc-pVDZ or MP2/cc-pVTZ). Right now, I
> don't truly know if the HF/6-31G(d) or MM results are correctly describing
> the shape of the PE curves. (However, from experience I believe that the QM
> results are correct.)
>
> The question now becomes is how important are these small conformational
> changes for your investigation. If they are very important, then you might
> have to do some parameter optimization.
>
> Hope this helps in thinking about your model.
>
> Bests,
> Karl
>
> On Tue, May 3, 2016 at 10:13 PM, conor parks <coparks2012.gmail.com>
> wrote:
>
> > David,
> >
> > thank you very much for providing that link. That was very helpful. That
> > clears up the negative sign issue for me. Thanks! Was my first question,
> > correct? I.E. the dihedral potential and forces get evaluated for each
> > parameter set associated with it, even when there are multiple, and the
> > results are summed?
> >
> > Regards,
> >
> > Conor Parks
> > B.S.E in Chemical Engineering, University of Michigan, 2012
> > PhD candidate in Chemical Engineering, Purdue University
> >
> > On Tue, May 3, 2016 at 3:53 PM, David A Case <david.case.rutgers.edu>
> > wrote:
> >
> > > On Tue, May 03, 2016, conor parks wrote:
> > > >
> > > > However, in my prmtop file (values given in first email in this
> chain),
> > > the
> > > > periodicity values are given as 1 and 2 (no negative sign). What
> > happened
> > > > to the negative sign on these periodicity values in my prmtop file?
> > >
> > > Please see http://ambermd.org/formats.html#parm.dat. Negative values
> > in a
> > > parm.dat file have a special meaning.
> > >
> > > ...dac
> > >
> > >
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>
>
> --
> Karl. N. Kirschner, Ph.D.
> Research Associate
> Bonn-Rhein-Sieg University of Applied Sciences
> Grantham-Allee 20, 54757 Sankt Augustin, Germany
>
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Received on Thu May 05 2016 - 16:30:02 PDT
