Colvars / examples
Example files for Colvars module: https://github.com/Colvars/colvars
☆12Updated 2 years ago
Related projects: ⓘ
- Python Tools for NAMD☆19Updated last year
- scripts for analyzing molecular dynamics trajectories using VMD☆35Updated 9 years ago
- Collection of Python scripts to setup and run simulations with OpenMM☆14Updated 4 years ago
- Python script that creates 2D protein-ligand interaction images☆14Updated 6 years ago
- A command line application to launch molecular dynamics simulations with OpenMM☆39Updated 2 years ago
- Calculation of water/solvent partition coefficients with Gromacs.☆25Updated 7 months ago
- Python library to run structure based model (SBM) simulations using the OpenMM toolkit☆21Updated 2 years ago
- Analysis of non-covalent interactions in MD trajectories☆51Updated last year
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆17Updated 4 years ago
- An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics☆15Updated 2 years ago
- Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.☆14Updated 6 years ago
- Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods☆19Updated 4 years ago
- ☆14Updated 2 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆30Updated last year
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆27Updated 7 months ago
- Repository for MD methods and analysis from submitted or published work☆17Updated last year
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆11Updated 5 years ago
- A Python program for QM/MM Simulations based on the Perturbed Matrix Method☆23Updated 11 months ago
- ☆25Updated 11 months ago
- An implementation of the 3SPN2 and 3SPN2.C coarse-grained DNA forcefields in OpenMM☆18Updated 4 months ago
- Scripts for PCA and related analyses of lipid motions☆10Updated 2 years ago
- This script makes a cyclic peptide or cyclic nucleotide topology file for GROMACS out of (specially prepared) linear molecule topology fi…☆9Updated 3 years ago
- ☆18Updated 2 years ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆51Updated 7 months ago
- We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…☆15Updated 2 months ago
- Examples of applications of pymbar to various problems in simulation and experiment☆16Updated 9 years ago
- Convenience functions for VMD-TCL scripting☆14Updated 4 years ago
- MMTSB Tool Set☆29Updated last month
- ☆11Updated 3 months ago
- Python code for generating Boresch restraints from MD simulations☆17Updated 2 years ago