PolyP3HT : Polymerize Atomistic P3HT

Handy script to generate topology and geometry files of arbitrarily long atomistic P3HT chains.

Two force fields are available:

1. The GROMOS 53A6-based parameters published in JACS 2017, 139, 3697-3705 - see the 2017RA-JACS folder;

2. The "Q-Forced" parameters (still relying on the GROMOS 53A6 Lennard-Jones parameters) published in Chemrxiv 2020 - see the 2020RA-qforce folder. This version improves the bonded parameters of P3HT, which were otherwise too flexible with the GROMOS standard parameters for angles and improper dihedrals in particular. This model is recommended for use in combination with subsequent quantum chemical calculations on the P3HT geometries (see, e.g, Chemrxiv 2020).

Both can be also downloaded from Figshare, which contains also a few example files obtained with the scripts. "Stable" releases will be uploaded to Figshare, while this repo is a good place where to raise issues or make improvements.

Use

cd 2017RA-JACS
./PolyP3HT.sh       12   # on Linux
./PolyP3HT-macOS.sh 12   # on macOS

where 12 is the desired number of monomers (note only that the number of monomers in the chain must be a multiple of 2). Note that the files shift-resnr.py, residuetypes.dat, p3ht_dimer_repeat_unit_50atoms.gro, header, and top2itp.sh must be in the folder where the script is being exectured along with the directory p3ht_gromos_v_2017RA-JACS.ff/ which contains the force field. The commands are analogous for the 2020RA-qforce version. The output files are in GROMACS format (itp and gro for the topology and geometry, respectively). More details are also included in the Supporting Information of Chemrxiv 2020.

License

Copyright 2018 University of Groningen

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

      http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.