shirtsgroup / cg_openmm
Tools to build coarse grained models and perform simulations with OpenMM
☆20Updated 2 years ago
Alternatives and similar repositories for cg_openmm:
Users that are interested in cg_openmm are comparing it to the libraries listed below
- ☆11Updated 8 months ago
- Cryptic pocket prediction using AlphaFold 2☆22Updated 2 years ago
- ☆27Updated last year
- Weighted Ensemble Data Analysis and Plotting☆23Updated 5 months ago
- Repo for the publication titled: "Key Interaction Networks: Identifying Evolutionarily Conserved Non-Covalent Interaction Networks Across…☆13Updated last year
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆12Updated 5 years ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆16Updated 3 months ago
- Bayesian Multistate Bennett Acceptance Ratio Method☆13Updated last month
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated this week
- This script makes a cyclic peptide or cyclic nucleotide topology file for GROMACS out of (specially prepared) linear molecule topology fi…☆12Updated 4 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- ☆32Updated 5 months ago
- ☆25Updated last year
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆13Updated last year
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆22Updated last month
- Add CMAP parameters into common AMBER prmtop file☆13Updated 3 years ago
- Temperature generator for Replica Exchange MD simulations☆27Updated 2 years ago
- Collection of Python scripts to setup and run simulations with OpenMM☆15Updated 4 years ago
- Fully automated high-throughput MD pipeline☆54Updated this week
- The public versio☆44Updated last year
- Python code for generating Boresch restraints from MD simulations☆18Updated 2 years ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆15Updated last year
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆36Updated last year
- A collections of scripts for working molecular dynamics simulations☆42Updated 8 months ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆27Updated last week
- ☆18Updated 3 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated last year
- ☆29Updated last year
- ☆13Updated 2 months ago