[gmx-users] Tacticity in polymer simulation

[Debadutta Prusty]

Sorry for posting the question here again. I cannot help but turn to this
forum since almost all papers I have read on tacticity in atomistic
simulations have used some kind of software package to build polymers with
desired tacticity. My university is banned from using Gaussian, which is
the most widely used package for generating such polymers. This prompted me
to  look for an algorithm that generates isotactic/syndiotactic/atactic
polymers. I have the pdb files for monomeric units (with two dangling bonds
to account for the bonds with neighbouring monomers). Now my polymer looks
like this: -CAH(R)-CBH2-CAH(R)-. I have a rough idea of how to go about
creating a polymer from a monomer. For example, if my program generates the
pdb file for the polymer by creating copies of the same monomer through the
translation of the CA atom along the x-axis keeping the relative
orientation of the other atoms (with respect to CA) the same for every
monomer, will I get an isotactic polymer ? If I flip the positions of R and
H for monomers adjacent to each other, will I get a syndiotactic polymer?
In my system, the adjacent monomeric units can be different (one charged,
another uncharged). How do I fix the angles that side groups make with the
plane containing the carbon atoms of the main chain.

Thanks,
Debadutta Prusty

On Thu, Jul 5, 2018 at 11:54 PM, Debadutta Prusty <
debaduttaprusty1.2015 at u.northwestern.edu> wrote:

> Hi everyone,
>
> How does one go about preparing a polymer in a given state of tacticity?
> From what I understand about tacticity in polymers, it boils down to
> coefficients(C1,C2,C3,C4,C5,C6) in Ryckaert-Bellemans function. If the
> potential well is not deep enough, the polymer can easily transition from
> an isotactic state into a syndiotactic state. The above coefficients for
> dihedral angles are fixed for a particular force field. I found a few
> papers on the effect of tacticity on properties of PAA,PMAA polymers where
> the pattern is CA(R)-CB-CA(R'), where R is the acid group. They do not
> mention whether it is the initial configuration that sets the tacticity of
> a polymer.  I am not sure how to keep the relative orientations of two R
> groups constant since they do not appear simultaneously in a dihedral
> pattern (the dihedrals are R-CA-CB-CA or CA-CB-CA-R' ). Any help would be
> appreciated.
>
> Thanks,
> Debadutta Prusty
>