Polymer-Maker

Package to create linear zwitterionic homopolymer structure and topology files for use with GROMACS OPLS-AA molecular dynamics simulations.

Made by Daniel Christiansen

Molecular Simulations Laboratory, University of Illinois at Chicago, Chicago, IL 60608

Usage

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Import polymer_maker with

from polymer_maker import polymer_maker

Create a polymer structure and system topology with

polymer_maker(n_polymers, angle)

Inputs

• polymer_formula - Text file describing the polymer to be made. See sample file for details
• n_polymers - Number of polymers to be in the final system
• angle - Degrees of rotation between neighboring monomers

Outputs

• newmol.gro - Structure file of polymer
• topol.top - Topology file for system
• newmol.itp - Topology file of polymer
• posre.itp - Atom position restraint file. Unimportant for most applications

Known issues:

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• Currently dependent on a fixed path to gmx (search for /usr/local/gromacs_gmx/bin/gmx in code)