moldyn / dcTMD
Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.
☆15Updated last week
Alternatives and similar repositories for dcTMD
Users that are interested in dcTMD are comparing it to the libraries listed below
Sorting:
- ☆11Updated 11 months ago
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- Tools to build coarse grained models and perform simulations with OpenMM☆23Updated 2 years ago
- Bayesian Multistate Bennett Acceptance Ratio Method☆13Updated last week
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆15Updated last year
- ☆28Updated last year
- ☆31Updated 7 months ago
- A tutorials suite for BioSimSpace.☆25Updated 2 weeks ago
- Python code for generating Boresch restraints from MD simulations☆20Updated 2 years ago
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆13Updated last year
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆31Updated last month
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last month
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated 2 years ago
- Density based object completion over PBC.☆30Updated 5 months ago
- Collection of Python scripts to setup and run simulations with OpenMM☆17Updated 4 years ago
- ☆35Updated 8 months ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated 6 months ago
- ☆25Updated last year
- Set up relative free energy calculations using a common scaffold☆22Updated 3 weeks ago
- Weighted Ensemble Data Analysis and Plotting☆24Updated 8 months ago
- ☆27Updated 11 months ago
- Toolkit for open antiviral drug discovery by the ASAP Discovery Consortium☆38Updated last month
- An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics☆15Updated 2 years ago
- Computation of the drug-target relative residence times from RAMD simulations☆16Updated 8 months ago
- The peleffy (PELE Force Field Yielder) is a Python package that builds PELE-compatible force field templates.☆12Updated last month
- Automatic Mutual Information Noise Omission☆15Updated 7 months ago
- Software for the prediction of DEER and PRE data from conformational ensembles.☆12Updated last week
- ☆27Updated this week