Utility scripts for MD data
Project description
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
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for md_utils-0.6.0-py2.py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 262e57bb1eb56c4e46715b9ff8deb466035662b9c12d102b2ad27cedc403e235 |
|
MD5 | ff5215f5f9aae524ca1acdc42439f995 |
|
BLAKE2b-256 | 508f62b66a62ccfc420fda365a56a7ac02635572388e3c0a6bc8adb69d8e3d39 |