md_utils 0.6.0

Utility scripts for MD data

Utility scripts for MD data

• Free software: BSD license

• Documentation: https://md_utils.readthedocs.org.

Scripts

fes_combo

Combines multiple FES output files into a single file so that the first column’s value is sequential. Files with higher starting index numbers are favored.

wham_split

Breaks wham input into increasingly smaller blocks (divide initial data set by 2, then 3, 4…) and creates wham input (meta) files and submit scripts.

wham_rad

Calculates the radially-corrected free energy values from WHAM output.

calc_pka

From the wham_rad output, calculates the pKa.

path_bin

Creates a summary VMD XYZ file (and separate log file) that averages a set of coordinates (one set of XYZ coordinates per line) from an input file.

press_dups

Compresses lines in a given CSV based on duplicate values in a specified column (RMSD by default) Compressed lines have their values averaged.

lammps_dist

Calculates the distances between a given set of atom pairs for each time step in a given LAMMPS dump file.

History

0.6.0 (2015-11-22)

• Added lammps_dist to calculate atom pair distances as found in a LAMMPS dump file.

0.5.0 (2015-11-21)

• Added press_dups to compress CSV rows that have duplicate values for a given column.

0.4.2 (2015-10-24)

• Added path_bin for creating an averaged VMD file from a larger set of coordinates.

0.4.1 (2015-10-10)

• Added max_loc and max_val columns to calc_pka output.

• Fixed problem with 0-start files in fes_combo.

0.4.0 (2015-10-01)

• Changed wham_rad to set the zero point at the the largest CV free E, rather than the max CV

0.3.0 (2015-09-07)

• Added wham_block.py

• Added wham_split.py

• Refactored common code to common and wham modules.

0.2.0 (2015-09-03)

• Added wham_rad.py

0.1.0 (2015-09-01)

• Renamed to md_utils

• Added fes_combo.py