https://github.com/mdsyn2019/research

PhD Molecular Dynamics Analysis Code - updated daily
https://github.com/mdsyn2019/research

chemistry molecular-dynamics molecular-modeling molecular-simulation

Last synced: about 2 months ago
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PhD Molecular Dynamics Analysis Code - updated daily

• Host: GitHub
• URL: https://github.com/mdsyn2019/research
• Owner: MDSYN2019
• Created: 2019-01-11T20:07:31.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2024-01-14T20:54:20.000Z (12 months ago)
• Last Synced: 2024-10-13T16:46:30.890Z (3 months ago)
• Topics: chemistry, molecular-dynamics, molecular-modeling, molecular-simulation
• Language: Roff
• Homepage:
• Size: 57.9 MB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 4
• Metadata Files:
  • Readme: README.md

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README

        
# Last Updated: 24/08/2021

# MD design in nanoparticles, free energy analysis of trajectories and other MPI/OpenMP files

CI link: https://travis-ci.com/MDSYN2019/PhD_work

 

[![

Build Status](https://travis-ci.com/MDSYN2019/PhD_work.svg?branch=master)](https://travis-ci.com/MDSYN2019/PhD_work)

PhD Molecular Dynamics analysis code 

This repository contains some of the code I used during period of my PhD, including free energy calculation codes, such as the Jarzynski Equality.

Work in this repository references the following works and books:

[1]. "Nonequilibrium equality for free energy differences", Phys Rev Lett, 78, 2690 

   

[2]. "Free energy reconstruction from nonequilibrium single-molecule pulling experiments", PNAS, 3658 - 3661, 98, 7, 2001

[3]. "Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality", Journal of Chemical Physics, 119, 6, 2003

 

[4]. "Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements", PNAS, 12564 - 12569, 100, 22, 2003 

-lQatPlotWidgets -lQt5PrintSupport -lQt5Svg -lQatPlotting -lQt5Widgets -lQatDataAnalysis -lQatGenericFunctions