Colvars / examplesLinks
Example files for Colvars module: https://github.com/Colvars/colvars
☆13Updated 3 years ago
Alternatives and similar repositories for examples
Users that are interested in examples are comparing it to the libraries listed below
Sorting:
- scripts for analyzing molecular dynamics trajectories using VMD☆39Updated 10 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated 2 years ago
- A collections of scripts for working molecular dynamics simulations☆44Updated last month
- Python Tools for NAMD☆21Updated 4 months ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Updated 10 years ago
- Main repository for METAGUI3☆20Updated 4 years ago
- Analysis of non-covalent interactions in MD trajectories☆62Updated 8 months ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Updated 6 years ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆22Updated 5 years ago
- A Python program for QM/MM Simulations based on the Perturbed Matrix Method☆26Updated last year
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆23Updated last year
- Multiscale Simulation Tool for Backmapping☆19Updated 2 weeks ago
- Collection of Python scripts to setup and run simulations with OpenMM☆17Updated 5 years ago
- Calculation of water/solvent partition coefficients with Gromacs.☆28Updated 11 months ago
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆29Updated last year
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Updated 2 years ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 3 years ago
- Pras Server is a library to repair PDB or mmCIF structures, add missing heavy atoms and hydrogen atoms and assign secondary structure by …☆28Updated last month
- ☆39Updated last year
- MMTSB Tool Set☆32Updated last month
- Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.☆14Updated 7 years ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆60Updated last year
- a VMD plugin for binding affinity prediction using end-point free energy methods☆27Updated 9 years ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated 3 weeks ago
- An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics☆15Updated 3 years ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆34Updated last year
- Temperature generator for Replica Exchange MD simulations☆29Updated 2 years ago
- PyRod - Tracing water molecules in molecular dynamics simulations☆50Updated 4 years ago
- Free Parametrization for Small Molecules☆36Updated 3 weeks ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago