molmod / openmm-tutorial-msbs
OpenMM tutorial for the MSBS course
☆156Updated this week
Alternatives and similar repositories for openmm-tutorial-msbs:
Users that are interested in openmm-tutorial-msbs are comparing it to the libraries listed below
- ☆123Updated 9 months ago
- the simple alchemistry library☆204Updated last month
- Describe and apply transformation on molecular structures and topologies☆105Updated this week
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆139Updated last month
- OFFICIAL: AnteChamber PYthon Parser interfacE☆214Updated last week
- Force fields produced by the Open Force Field Initiative☆143Updated 3 weeks ago
- PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.☆135Updated last month
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆173Updated last year
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆185Updated this week
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆126Updated last week
- Auto3D generates low-energy conformers from SMILES/SDF☆154Updated 5 months ago
- Scoring of shape and ESP similarity with RDKit☆208Updated last year
- PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.☆276Updated 11 months ago
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆271Updated 3 weeks ago
- Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196☆222Updated 2 months ago
- binding free energy estimator 2☆109Updated last month
- LiveCoMS GROMACS Tutorials Paper☆110Updated 5 years ago
- PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.☆130Updated this week
- Some useful RDKit functions☆153Updated last month
- gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.☆236Updated last week
- Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates☆130Updated 3 months ago
- An open tool implementing some recommended practices for analyzing alchemical free energy calculations☆124Updated 8 months ago
- ☆51Updated last year
- Benchmark set for relative free energy calculations.☆103Updated 8 months ago
- A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.☆257Updated this week
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆183Updated last year
- CReM: chemically reasonable mutations framework☆214Updated last month
- Simple protein-ligand complex simulation with OpenMM☆74Updated last year
- Protein-Ligand Benchmark Dataset for Free Energy Calculations☆161Updated 6 months ago
- Interface for AutoDock, molecule parameterization☆219Updated this week