melomcr / dynetan
Python implementation of Dynamical Network Analysis
☆13Updated last year
Related projects ⓘ
Alternatives and complementary repositories for dynetan
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆41Updated 3 years ago
- ☆29Updated last month
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆70Updated 5 months ago
- ☆53Updated last year
- ☆39Updated 4 months ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆43Updated 2 weeks ago
- Set up relative free energy calculations using a common scaffold☆22Updated 3 months ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆53Updated last year
- An OpenMM plugin that implements the Alchemical Transfer Potential☆37Updated last year
- Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface☆31Updated 3 years ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆60Updated last year
- The public versio☆36Updated last year
- ☆49Updated last year
- Random Acceleration Molecular Dynamics in GROMACS☆32Updated 4 months ago
- An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics☆15Updated 2 years ago
- Force fields in various formats☆26Updated 6 months ago
- Tool to predict water molecules placement and energy in ligand binding sites☆27Updated 4 months ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆30Updated last year
- ☆71Updated last year
- A python implementation of the string method with swarms of trajectories using GROMACS☆17Updated 2 years ago
- binding free energy estimator 2☆108Updated last week
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated 11 months ago
- ☆62Updated 4 months ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆14Updated last year
- Temperature generator for Replica Exchange MD simulations☆25Updated last year
- Thompson Sampling☆55Updated this week
- Python code for generating Boresch restraints from MD simulations☆18Updated 2 years ago
- A tool for setting up free energy simulations.☆34Updated 2 years ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆63Updated last year