moldyn / dcTMDLinks
Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.
☆15Updated 4 months ago
Alternatives and similar repositories for dcTMD
Users that are interested in dcTMD are comparing it to the libraries listed below
Sorting:
- Python code for generating Boresch restraints from MD simulations☆22Updated 3 years ago
- ☆34Updated 11 months ago
- ☆39Updated last year
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆18Updated 2 years ago
- Temperature generator for Replica Exchange MD simulations☆29Updated 2 years ago
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆40Updated 2 weeks ago
- Random Acceleration Molecular Dynamics in GROMACS☆39Updated last year
- Computation of the drug-target relative residence times from RAMD simulations☆16Updated last year
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- Cryptic pocket prediction using AlphaFold 2☆24Updated 2 years ago
- ☆69Updated last year
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- A python module to plot secondary structure schemes☆25Updated last year
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆31Updated last year
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆49Updated 4 years ago
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆15Updated 3 years ago
- ☆28Updated last year
- Bayesian Multistate Bennett Acceptance Ratio Method☆15Updated this week
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last month
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- Force Fields☆65Updated 7 months ago
- MDANCE is a flexible n-ary clustering package for all applications.☆70Updated last week
- ☆65Updated last month
- A simple implementation of replica exchange MD simulations for OpenMM.☆23Updated 4 years ago
- Useful Collective Variables for OpenMM☆14Updated last year
- BitBIRCH-Lean, a memory-efficient implementation of BitBIRCH designed for high-thorouput clustering of huge molecular libraries (up to hu…☆20Updated this week
- Tools to build coarse grained models and perform simulations with OpenMM☆24Updated 2 years ago
- An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics☆15Updated 3 years ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆83Updated 2 months ago
- A tutorials suite for BioSimSpace.☆26Updated 4 months ago