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

David L. Bostick dbostick at physics.unc.edu
Fri Aug 30 22:54:51 CEST 2002


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

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

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

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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