Polymerize Atomistic P3HT

Script to generate topology and geometry files of arbitrarily long P3HT chains (note only that the number of monomers in the chain <b>must</b> be a multiple of 2). The output files are in GROMACS format (itp and gro for the topology and geometry, respectively).<br><br>The standard version of the script works on Linux. There is also a version which runs on macOS.<br><br>Use:<br>unzip PolyP3HT.zip<br>./PolyP3HT.sh 12<br><br>where 12 is the desired number of monomers.<br>Make sure the files <i>shift-resnr.py</i>, <i>residuetypes.dat</i>, <i>p3ht_dimer_repeat_unit_50atoms.gro</i>, <i>header</i>, and <i>top2itp.sh</i> are in the folder where the script is being executed along with the directory <b>p3ht_gromos_v_2017RA-JACS.ff/ </b>which contains the force field. The force field is the one published in Ref. [<i>J. Am. Chem. Soc.</i>, <b>2017</b>, 139 (10), pp 3697–3705].<br><br>For an example on how to employ the force field, see:<br>https://figshare.com/articles/P3HT_and_PCBM_atomistic_force_fields/5051593<br><br>There is also an <i>example-outcome.zip</i> archive where files which should be obtained in the case of a 4-mer and 14-mer if the script runs fine.<br>本脚本用于生成长度任意的聚3-己基噻吩（P3HT）链的拓扑与几何结构文件（注意：链内单体数目必须为2的整数倍）。输出文件采用GROMACS格式，分别为拓扑文件itp与几何结构文件gro。 本脚本的标准版本适配Linux操作系统，另有适配macOS系统的版本。 使用方式： unzip PolyP3HT.zip ./PolyP3HT.sh 12 其中12为所需的单体总数。 请确保以下文件与文件夹均存在于脚本运行的工作目录中：shift-resnr.py、residuetypes.dat、p3ht_dimer_repeat_unit_50atoms.gro、header、top2itp.sh，以及存储力场文件的文件夹p3ht_gromos_v_2017RA-JACS.ff/。该力场刊发于文献《美国化学会志》（J. Am. Chem. Soc.），2017年，第139卷第10期，第3697–3705页。 如需参考该力场的使用示例，可访问以下链接： https://figshare.com/articles/P3HT_and_PCBM_atomistic_force_fields/5051593 另有example-outcome.zip压缩包，内含脚本正常运行时，生成4聚体与14聚体P3HT链所应得到的结果文件。