Panda-DaLong's repositories
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.
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