[gmx-users] poly(lactic acid) .itp or .top file

[David L. Bostick]

Oh.. a correction,

You can only do this on a molecule for which only one proper dihedral is
missing.  This is why most of the time a large molecule is broken down into
smaller ones which are analogs of parts of the larger one for QM
calculations.

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David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick
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On Fri, 30 Aug 2002, David L. Bostick wrote:

>
> Hi
>
> If you have parameters for most of the dihedrals except for a few for which
> you have QM data.. i.e. energy as a function of the rotation of the
> dihedral.  Then you need to input the single point conformations for each
> value of the dihedral angle for which you have the energy into gromacs.
> You must build a topology .itp file for the molecule with all parameters
> you wish to use .. bonds, angles, charges, etc except for the dihedrals
> which may appear, but have barrier constants of 0.0 .   Evaluate the energy
> for each of these conformations.  Then you can produce an energy difference
> profile by subtracting this "gromacs" energy from the QM energy profile as
> a function of theta (dihedral angle).  It is to this profile you may fit a
> series of dihedral functions using some fitting program.  Since you are
> using Gromacs, you should use only one dihedral function for the fit.  If
> you need a series of them, then you should switch to fitting a function of
> the form of Ryckaert-Bellemans .. see the manual on dihedral potential
> forms.
>
> Then go back and test the fit by evaluating the gromacs energy with the
> determined dihedral barrier values, phases, and periodicities for the
> configurations again and view them side by side with the QM data for
> validation.  For a complicated dihedral energy profile, this can take a
> while, but for easy ones you may get it on the first try.  To evaluate the
> energy in gromacs you need to not use periodic boundaries and not use
> cutoffs .. simply calculate the entire intrinsic potential of the molecule
> given the configuration.
>
> If you want to be sure about impropers, I have not done this before, but I
> think you can just steal something reasonable from existing (as
> analogous as possible) ffgmx parameters before you fit your improper
> dihedrals.
>
> David
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> David Bostick					Office: 262 Venable Hall
> Dept. of Physics and Astronomy			Phone:  (919)962-0165
> Program in Molecular and Cellular Biophysics
> UNC-Chapel Hill
> CB #3255 Phillips Hall				dbostick at physics.unc.edu
> Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick
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>
> On Fri, 30 Aug 2002, Chris O'Brien wrote:
>
> > Hello all,
> >
> > I am trying to develop an accurate topology file for poly(lactic acid).
> > Most features of the topology file are obvious, but I have some questions
> > about the dihedral parameters. How do I take quantum modeling (MP2 and DFT
> > level) information about the barrier for rotating the dihedral angle and
> > convert that into the parameters listed in the .itp file?
> >
> > Same question for the improper dihedrals.  How important is the force
> > constant value to successful modeling?  Can you just make it large to
> > discourage (for example) a change of chirality?  If it is important to have
> > these numbers accurately, does anybody know the best way to calculate them?
> >
> > Thank you,
> >
> > Chris O'Brien
> > Clemson University
> >
> >
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