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[Licence| Download | New Version Template] aejh_v2_0.tar.gz(8318 Kbytes)
Manuscript Title: Modular reweighting software for statistical mechanical analysis of biased equilibrium data
Authors: Daniel J. Sindhikara
Program title: Modular reweighting version 2
Catalogue identifier: AEJH_v2_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 183(2012)1560
Programming language: C++, Python 2.6+, Perl 5+.
Computer: Any.
Operating system: Any.
RAM: 50-500MB
Supplementary material: An updated version of the original manuscript (Comput. Phys. Commun. 182(2011)2227) is available.
Keywords: Statistical reweighting, WHAM, REMD, Replica exchange, Mbrella sampling, Bootstrap resampling, Enhanced sampling algorithm, Generalized-ensemble algorithm.
PACS: 05.10.-a, 07.05.Kf, 07.05.Tp.
Classification: 4.13.

Does the new version supersede the previous version?: Yes

Nature of problem:
While equilibrium reweighting is ubiquitous, there are no public programs available to perform the reweighting in the general case. Further, specific programs often suffer from many library dependencies and numerical instability.

Solution method:
This package is written in a modular format that allows for easy applicability of reweighting in the general case. Modules are small, numerically stable, and require minimal libraries.

Reasons for new version:
Some minor bugs, some upgrades needed, error analysis added.

Summary of revisions:
  1. analyzeweight.py/analyzeweight.py2 has been replaced by "multihist.py" This new program performs all the functions of its predecessor while being versatile enough to handle other types of histograms and probability analysis.
  2. "bootstrap.py" was added. This script performs basic bootstrap resampling allowing for error analysis of data.
  3. "avg_dev_distribution.py" was added. This program computes the averages and standard deviations of multiple distributions, making error analysis (e.g. from bootstrap resampling) easier to visualize.
  4. WRE.cpp was slightly modified purely for cosmetic reasons.
  5. The manual was updated for clarity and to reflect version updates. Examples were removed from the manual in favor of online tutorials (packaged examples remain).
  6. Examples were updated to reflect the new format. An additional example is included to demonstrate error analysis

Running time:
Preprocessing scripts 1-5 minutes, WHAM engine < 1 minute, postprocess script ~ 1-5 minutes.