moldyn / dcTMDLinks
Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.
☆16Updated last month
Alternatives and similar repositories for dcTMD
Users that are interested in dcTMD are comparing it to the libraries listed below
Sorting:
- An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics☆17Updated 3 years ago
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 4 years ago
- A tutorials suite for BioSimSpace.☆34Updated 3 months ago
- Entropy from PDB conformational ensembles☆13Updated last year
- Computation of the drug-target relative residence times from RAMD simulations☆21Updated last year
- Bayesian Multistate Bennett Acceptance Ratio Method☆16Updated 3 months ago
- ☆43Updated last year
- Tools to build coarse grained models and perform simulations with OpenMM☆25Updated 3 years ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆19Updated 2 years ago
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆16Updated 4 years ago
- ☆35Updated last year
- ☆32Updated 2 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated 2 years ago
- Python code for generating Boresch restraints from MD simulations☆22Updated 3 months ago
- Set up relative free energy calculations using a common scaffold☆24Updated 5 months ago
- ☆31Updated 2 weeks ago
- Temperature generator for Replica Exchange MD simulations☆29Updated 3 years ago
- Random Acceleration Molecular Dynamics in GROMACS☆43Updated last year
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆49Updated 4 years ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆72Updated last week
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆32Updated 8 months ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Updated 2 years ago
- Free Parametrization for Small Molecules☆50Updated this week
- ☆13Updated 6 months ago
- Dynamic pharmacophore modeling of molecular interactions☆38Updated last year
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆31Updated 2 years ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆18Updated this week
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆43Updated 2 months ago
- Cryptic pocket prediction using AlphaFold 2☆24Updated 3 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆40Updated 2 years ago