Colvars / examplesLinks
Example files for Colvars module: https://github.com/Colvars/colvars
☆13Updated 4 years ago
Alternatives and similar repositories for examples
Users that are interested in examples are comparing it to the libraries listed below
Sorting:
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆39Updated 2 years ago
- Python Tools for NAMD☆23Updated 7 months ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆24Updated 6 years ago
- scripts for analyzing molecular dynamics trajectories using VMD☆39Updated 10 years ago
- A collections of scripts for working molecular dynamics simulations☆44Updated 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
- 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
- Analysis of non-covalent interactions in MD trajectories☆65Updated 11 months ago
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆29Updated last year
- easyPARM is a computational tool developed to simplify the derivation of force field parameters for metal-containing molecular systems an…☆30Updated 3 weeks ago
- Calculation of water/solvent partition coefficients with Gromacs.☆28Updated last year
- Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods☆19Updated 6 years ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆35Updated 2 years ago
- An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics☆17Updated 3 years ago
- Collection of Python scripts to setup and run simulations with OpenMM☆17Updated 5 years ago
- A tutorials suite for BioSimSpace.☆31Updated last month
- This script makes a cyclic peptide or cyclic nucleotide topology file for GROMACS out of (specially prepared) linear molecule topology fi…☆14Updated 5 years ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Updated 6 years ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆63Updated last year
- Tutorials on doing AMBER based Metadynamics and Gaussian Accelerated MD (GaMD)☆11Updated 2 weeks ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Updated 3 years ago
- Workshop - Analysis of Molecular Dynamics Simulation Using Python☆19Updated 5 years ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆33Updated last week
- A Python program for QM/MM Simulations based on the Perturbed Matrix Method☆26Updated 2 years ago
- Temperature generator for Replica Exchange MD simulations☆29Updated 3 years ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆18Updated 2 months ago
- Multiscale Simulation Tool for Backmapping☆22Updated 3 months ago
- Automatic CHARMM-GUI browser interaction with Python☆17Updated 2 years ago
- Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over pop…☆62Updated last month