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abf-example-files-for-namd-and-openmm

awesome-cheatsheets

超级速查表 - 编程语言、框架和开发工具的速查表，单个文件包含一切你需要知道的东西 :zap:

cnt-lipid14-analysis

Analysis tools for simulations of carbon nanotubes (CNTs) in lipid membranes modeled with the Lipid14 force field.

cnt_milestoning_method

frontier-expansion-sampling

jarzynski

Simulations based on Jarzynski's inequality for an Advanced Statistical Physics course

md-permeation

MD-permeation: a FORTRAN code to analyze MD simulation trajectories and identify permeation events for water molecules. List of Authors Carlos R. S. Camilo, José R. Ruggiero, Alexandre S. de Araujo Department of Physics, IBILCE, São Paulo State University (UNESP) Citation If you use MD-permeation in your research, we ask that you cite the following article: C.R.S. Camilo, J.R. Ruggiero, and A.S. de Araujo. 2021. A method for detection of permeation events in Molecular Dynamics simulations of lipid bilayers. bioRxiv doi:10.1101/2021.01.20.427278

md_methods-and-analysis

Repository for MD methods and analysis from submitted or published work

mdnotebooks

Jupyter Notebooks for Molecular Dynamics

miniomm

A simple OpenMM wrapper for common-case MD runs

openmm-customtools

Some CustomBond and CustomIntegrator classes for collective varible defining and enhanced sampling

openmm-scripts-amoeba

:microscope: OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field

openmm-tutorial-msbs

OpenMM tutorial for the MSBS course

openmmforcefields

CHARMM and AMBER forcefields for OpenMM (with small molecule support)

software-development

A primer on software development best practices for computational chemistry

solvation-analysis

A set of functions and analysis classes for solvation structure analysis