MiaoLab20 / gamd-openmm
Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calculations of biomolecules. It works by adding a harmonic boost potential to smooth the potential energy surface and reduce system energy barriers. http://miao.compbio.ku.edu/GaMD/
☆81Updated last week
Alternatives and similar repositories for gamd-openmm:
Users that are interested in gamd-openmm are comparing it to the libraries listed below
- A python toolkit for analysing membrane protein-lipid interactions.☆63Updated 2 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated 2 years ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆62Updated last year
- binding free energy estimator 2☆113Updated last week
- ☆68Updated 10 months ago
- ☆54Updated 2 years ago
- ☆31Updated 6 months ago
- Simple protein-ligand complex simulation with OpenMM☆84Updated last year
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆75Updated last year
- The public versio☆52Updated last year
- ☆57Updated last year
- Random Acceleration Molecular Dynamics in GROMACS☆36Updated 9 months ago
- Trusted force field files for gromacs☆47Updated 6 months ago
- Computational Chemistry Workflows☆54Updated 2 years ago
- ☆58Updated last week
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆48Updated last month
- A python module to plot secondary structure schemes☆25Updated last year
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆61Updated 3 months ago
- ☆64Updated last year
- Fully automated high-throughput MD pipeline☆60Updated this week
- Gypsum-DL is a free, open-source program that converts 1D and 2D small-molecule representations (SMILES strings or flat SDF files) into 3…☆53Updated 3 months ago
- ☆39Updated 9 months ago
- EnzyHTP is a python library that automates the complete life-cycle of enzyme modeling☆21Updated last week
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆45Updated 4 years ago
- ☆49Updated 2 months ago
- The Free Energy Landscape Analysis tool offers a comprehensive suite for analyzing and visualizing the free energy landscape derived from…☆20Updated 2 months ago
- ☆13Updated this week
- Python tutorial for estimating and clustering free energy landscapes with InfleCS.☆28Updated 3 years ago
- BitBIRCH clustering algorithm☆69Updated last month
- Automated Adaptive Absolute alchemical Free Energy calculator☆92Updated last week