Paper Citing NAMD - Abstract
Hosek, Petr; Spiwok, Vojtech
Metadyn View: Fast web-based viewer of free energy surfaces calculated by metadynamics
COMPUTER PHYSICS COMMUNICATIONS, 198:222-229, JAN 2016
Metadynamics is a highly successful enhanced sampling technique for simulation of molecular processes and prediction of their free energy surfaces. An in-depth analysis of data obtained by this method is as important as the simulation itself. Although there are several tools to compute free energy surfaces from metadynamics data, they usually lack user friendliness and a build-in visualization part. Here we introduce Metadyn View as a fast and user friendly viewer of bias potential/free energy surfaces calculated by metadynamics in Plumed package. It is based on modern web technologies including HTML5JavaScript and Cascade Style Sheets (CSS). It can be used by visiting the web site and uploading a HILLS file. It calculates the bias potential/free energy surface on the client-side, so it can run online or offline without necessity to install additional web engines. Moreover, it includes tools for measurement of free energies and free energy differences and data/image export. Program summary Program title: Metadyn View Catalogue identifier: AEYC_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEYC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL v3.0 No. of lines in distributed program, including test data, etc.: 273269 No. of bytes in distributed program, including test data, etc.: 4632839 Distribution format: tar.gz Programming language: HTML5, JavaScript, CSS, WebGL. Computer: Any computer with a modern web browser compatible with HTML5, JavaScript and CSS. Operating system: Platform-independent. RAM: Depends on the number of Gaussian hills and dimensionality of the bias potential. Classification: 3, 7.7, 23. Nature of problem: Fast and interactive visualization of free energy surfaces of molecular systems calculated by metadynamics method. Solution method: Implementation of optimized Bias Sum algorithm and a set of tools for free energy surface analysis. Unusual features: The program, due to its web-based nature, can be run on a wide range of devices and without installation. Running time: Couple of seconds for a medium sized HILLS file (tens of thousands of lines). (C) 2015 Elsevier B.V. All rights reserved.
