From e2c6c8f589a63fd1053262f19459bf9f898e8005 Mon Sep 17 00:00:00 2001 From: Daniel Bauer Date: Tue, 13 Nov 2018 12:22:09 +0100 Subject: [PATCH 1/3] typos --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index c15eb84..76fb42a 100644 --- a/README.md +++ b/README.md @@ -4,8 +4,8 @@ Weighted Histogram Analysis Method (WHAM) === This is an fast implementation of the weighted histogram analysis method written in Rust. It allows the calculation of multidimensional free energy profiles -from umbrella sampling simulations. For more details on the method, I suggest Roux, B. -(1995). The calculation of the potential of mena force using computer simulations, CPC, 91(1), 275-282. +from umbrella sampling simulations. For more details on the method, I suggest *Roux, B. +(1995). The calculation of the potential of mean force using computer simulations, CPC, 91(1), 275-282.* Features --- @@ -74,8 +74,8 @@ Error analysis WHAM can perform error analysis using the bayesian bootstrapping method. Every simulation window is assumed to be an individual set of data point. By calculating probabilities N times with randomly assigned weights for each window, one can estimate the error as standard deviation between the N bootstrapping runs. For more details see -van der Spoel, D. et al. (2010). g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and -Autocorrelation Estimates, JCTC, 6(12), 3713-3720. +*Van der Spoel, D. et al. (2010). g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and +Autocorrelation Estimates, JCTC, 6(12), 3713-3720*. To perform bayesian bootstrapping in WHAM, use the ```-bt ``` flag to perform individual bootstrapping runs. The error estimates of bin probabilities and free energy will be given as separate column (+/-) in the output file. From b15cfde8f1def2abacb54dbd143cde29bccfb8f7 Mon Sep 17 00:00:00 2001 From: Daniel Bauer Date: Tue, 13 Nov 2018 12:24:01 +0100 Subject: [PATCH 2/3] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 76fb42a..9028309 100644 --- a/README.md +++ b/README.md @@ -101,4 +101,4 @@ WHAM is licensed under the GPL-3.0 license. Please read the LICENSE file in this repository for more information. Parts of this work, especially some perfomance optimizations and the I/O format, are inspired by the -implementation of A. Grossfield (*A. Grossfield, "WHAM: the weighted histogram analysis method", http://membrane.urmc.rochester.edu/content/wham*). +implementation of A. Grossfield (*Grossfield, A, WHAM: the weighted histogram analysis method, http://membrane.urmc.rochester.edu/content/wham*). From 5caa2b5f20bedcfa157e43620c2155538c67e51f Mon Sep 17 00:00:00 2001 From: Daniel Bauer Date: Thu, 15 Nov 2018 10:19:39 +0100 Subject: [PATCH 3/3] DOI --- README.md | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 9028309..dd5e2f5 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,6 @@ -[![Build Status](https://travis-ci.com/danijoo/WHAM.svg?branch=master)](https://travis-ci.com/danijoo/WHAM) [![crates.io](https://img.shields.io/badge/crates.io-orange.svg?longCache=true)](https://www.crates.io/crates/wham) +[![Build Status](https://travis-ci.com/danijoo/WHAM.svg?branch=master)](https://travis-ci.com/danijoo/WHAM) [![crates.io](https://img.shields.io/badge/crates.io-orange.svg?longCache=true)](https://www.crates.io/crates/wham) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1488598.svg)](https://doi.org/10.5281/zenodo.1488598) + + Weighted Histogram Analysis Method (WHAM) === @@ -95,10 +97,12 @@ TODO - Autocorrelation - Replica exchange -License +License & Citing --- WHAM is licensed under the GPL-3.0 license. Please read the LICENSE file in this repository for more information. +There's no publication for this WHAM implementation. However, there is a citeabe DOI. If you use this software for your work, please consider citing it: *Bauer, D, WHAM - An efficient weighted histogram analysis implementation written in Rust, Zenodo. https://doi.org/10.5281/zenodo.1488597* + Parts of this work, especially some perfomance optimizations and the I/O format, are inspired by the implementation of A. Grossfield (*Grossfield, A, WHAM: the weighted histogram analysis method, http://membrane.urmc.rochester.edu/content/wham*).