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Polymerize Atomistic P3HT
Version 3 2020-05-23, 15:57
Version 2 2018-02-19, 19:05
Version 1 2018-02-04, 14:33
software
posted on 2020-05-23, 15:57 authored by Riccardo AlessandriRiccardo Alessandri, Selim Sami, Jonathan BarnoudJonathan Barnoud, Alex H. de Vries, Siewert
J. Marrink, Remco W. A. HavenithScript to generate topology and geometry files of arbitrarily long P3HT chains (note only that the number of monomers in the chain must be a multiple of 2). The output files are in GROMACS format (itp and gro for the topology and geometry, respectively).
Force fields:
Use:
unzip PolyP3HT.zip
Force fields:
Two force fields are available:
1. The GROMOS 53A6-based parameters published in [JACS, 2017, DOI: 10.1021/jacs.6b11717];
2. The "Q-Forced" parameters (still relying on the GROMOS 53A6 Lennard-Jones parameters) published in [Chemrxiv 2020, DOI: 10.26434/chemrxiv.12277931]; this version is recommended for use in combination with subsequent quantum chemical calculations.
unzip PolyP3HT.zip
cd 2017RA-JACS
./PolyP3HT.sh 12
where 12 is the desired number of monomers. 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 executed along with the directory p3ht_gromos_v_2017RA-JACS.ff/ which contains the force field. The commands are analogous for the 2020RA-qforce version.
./PolyP3HT.sh 12
where 12 is the desired number of monomers. 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 executed 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 standard version of the script runs on Linux. A version which runs on macOS is also included.
The example-outcome.zip contains the files which should be obtained in the case of a 6-mer and 16-mer if the script runs fine (in both force field versions).
The example-outcome.zip contains the files which should be obtained in the case of a 6-mer and 16-mer if the script runs fine (in both force field versions).
More:
To contribute or raise an issue, here's a GitHub page: https://github.com/ricalessandri/PolyP3HT
Finally, for an example on how to employ the force field, see:
https://doi.org/10.6084/m9.figshare.5051593
