venus-trjconv

A VENUS96 trajectory converter

Author: mizu-bai

Requirements

• Python 3.8 and above
• Numpy

Features

venus-trjconv can convert VENUS96 trajectories to gro, g96, and xyz format, making it easier to visualize and analyze the trajectories calculated by VENUS96.

Usage

$ python3 -m venus_trjconv -h
usage: venus_trjconv [-h] -f F [-s S] [-o O] [-dt DT] [-r R]

Convert VENUS96 trajectory to other formats.

optional arguments:
  -h, --help  show this help message and exit
  -f F        Trajectory: VENUS96 output
  -s S        Structure: gro xyz
  -o O        Trajectory: gro g96 xyz
  -dt DT      Only write frame when t MOD dt = first time (ps)
  -r R        Reorder file

Example

In folder example/, there is a QCT trajectory of methane molecule.

• ch4.dt5: VENUS96 input file.
• ch4.out: VENUS96 output file, containing 5 trajectories.
• template.gro: Gro file, venus_trjconv will read the title, number of atoms, residue numbers, residue names, atom names, atom numbers and box size stored in it.
• template.xyz: XYZ file, venus_trjconv will read the title, number of atoms stored in it.
• reorder.txt: In VENUS96 output, the order of atoms is H H H H C, while it is supposed to be C H H H H in converted trajectories. Thus, a reorder file should be supplied. In the reorder.txt file, the first line is 5, indicating that the 5th atom (C) in VENUS96 output should be the 1st atom in converted trajectories. If the order of atoms in the VENUS96 output is correct, the reorder file and -r option are not necessary.

Convert to gro

$ python3 -m venus_trjconv -f ch4.out -s template.gro -o gro/ch4_traj.gro -r reorder.txt

Convert to g96

$ python3 -m venus_trjconv -f ch4.out -o g96/ch4_traj.g96 -r reorder.txt

Convert to xyz

$ python3 -m venus_trjconv -f ch4.out -s template.xyz -o xyz/ch4_traj.xyz -r reorder.txt

Reference

(1) Hase, W. L.; Duchovic, R. J.; Hu, X.; Komornicki, A.; Lim, K. F.; Lu, D.-H.; Peslherbe, G. H.; Swamy, K. N.; Vande Linde, S. R.; Varandas, A., Wang, H.; Wolf, R. J. VENUS96: A general chemical dynamics computer program, Quantum Chemical Program Exchange (QCPE) Bulletin, 1996, 16 (4), 671. https://www.depts.ttu.edu/chemistry/Venus/index.php

(2) Abraham, M. J.; Murtola, T.; Schulz, R.; Páll, S.; Smith, J. C.; Hess, B.; Lindahl, E. GROMACS: High Performance Molecular Simulations through Multi-Level Parallelism from Laptops to Supercomputers. SoftwareX 2015, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001.

(3) Scott, W. R. P.; Hünenberger, P. H.; Tironi, I. G.; Mark, A. E.; Billeter, S. R.; Fennen, J.; Torda, A. E.; Huber, T.; Krüger, P.; van Gunsteren, W. F. The GROMOS Biomolecular Simulation Program Package. J. Phys. Chem. A 1999, 103 (19), 3596–3607. https://doi.org/10.1021/jp984217f.

License

BSD-2-Clause license