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Analysis libraries for molecular trajectories: a cross-language synopsis

zotfile_doctor

Zotfile directory consistency checker

Python

vmd_density_profile

Computing 1-D atomic densities in macromolecular simulations: The density profile tool for VMD.

Tcl

vmd_diffusion_coefficient

Computing Diffusion Coefficients in Macromolecular Simulations: The Diffusion Coefficient Tool for VMD

Tcl

vmd_plumed

Main code repository for the PLUMED-GUI plugin for VMD

Tcl

miniomm

A simple OpenMM wrapper for common-case MD runs

Python

vmd_misc

Development branch - not for general use

Perl

openmm-plumed-tests

Alanine dipeptide OpenMM-Plumed test

Rich Text Format

ACEMD-PLUMED

Running biased simulations with PLUMED and ACEMD

Gnuplot

CHARMM_GUI_GROMACS_5_fixup

Fixup for CHARMM-GUI and GROMACS5

Shell

2017-PLUMED-workshop

Raw material for the presentation at the PLUMED 2017 workshop in Trieste

Python

2019-Markov-Tutorial-UniMi

Material for the Markov + MD Lecture @ Unimi

HTML

2021-Markov-Tutorial-BCN

Material for the Markov + MD Lecture @ Master MSI Barcelona

Jupyter Notebook

2022-MD-Trajectory-Tutorial-UniPD

For Prof. Fuxreiter's course

Jupyter Notebook

2023-Markov-Tutorial-UniPD

Markov tutorial for prof. Fuxreiter's course.

Jupyter Notebook

2020-Markov-Tutorial-BCN

Material for the Markov + MD Lecture @ Master MSI Barcelona

Jupyter Notebook

2019-Markov-Tutorial-BCN

Material for the Markov + MD Lecture @ Master MSI Barcelona

HTML

2019-PlumedAutoDiff-Lugano

Code accompanying my talk at *Open source software for enhanced-sampling simulations*

Jupyter Notebook

2023-OpenMM-MD-UniPD

For prof. Fuxreiter's Course

giorginolab/analysis_libraries_chapter

giorginolab

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