Modular reweighting software for statistical mechanical analysis of biased equilibrium data

Abstract

Here a simple, useful, modular approach and software suite designed for statistical reweighting and analysis of equilibrium ensembles is presented. Statistical reweighting is useful and sometimes necessary for analysis of equilibrium enhanced sampling methods, such as umbrella sampling or replica exchange, and also in experimental cases where biasing factors are explicitly known. Essentially, statistical reweighting allows extrapolation of data from one or more equilibrium ensembles to another. Here, the fundamental separable steps of statistical reweighting are broken up into modules – allowing for application to the general case and avoiding the black-box nature of some “all-inclusive” reweighting programs. Additionally, the programs included are, by-design, written with little dependencies. The compilers required are either pre-installed on most systems, or freely available for download with minimal trouble. Examples of the use of this suite applied to umbrella sampling and replica exchange molecular dynamics simulations will be shown along with advice on how to apply it in the general case. Program summaryProgram title: Modular reweighting software for statistical mechanical analysis of biased equilibrium dataCatalogue identifier: AEJH_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJH_v1_0.htmlProgram obtainable from: CPC Program Library, Queenʼs University, Belfast, N. IrelandLicensing provisions: GNU General Public License v3.0No. of lines in distributed program, including test data, etc.: 2 089 136No. of bytes in distributed program, including test data, etc.: 21 104 847Distribution format: tar.gzProgramming language: C/C++/python3.x/python2.xComputer: AnyOperating system: Linux/Mac OSXRAM: 50–500 MBClassification: 4.13External routines: python3: math, os.path; c compiler: math.h, string.h, stdio.h, stdlib.hNature 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.Running time: Preprocessing scripts 1–5 minutes, WHAM engine < 1 minute, postprocess script < 1 minute.