RyanLeeHayes / ALF
Adaptive landscape flattening scripts for MSLD
☆14Updated 8 months ago
Alternatives and similar repositories for ALF:
Users that are interested in ALF are comparing it to the libraries listed below
- BLaDE is a Basic Lambda Dynamics Engine for molecular dynamics based alchemical free energy calculations using multisite lambda dynamics …☆18Updated last month
- Accurate prediction of protein pKa with representation learning☆42Updated 2 weeks ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated last year
- The public versio☆47Updated last year
- Python code for generating Boresch restraints from MD simulations☆19Updated 2 years ago
- Different run and analysis scripts as described in the research guides.☆13Updated 2 years ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆43Updated 4 years ago
- A python implementation of the string method with swarms of trajectories using GROMACS☆18Updated 2 years ago
- Set up relative free energy calculations using a common scaffold☆22Updated 6 months ago
- ☆55Updated last year
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆46Updated 4 months ago
- Repository for the 2024 OpenFE industry benchmark efforts☆13Updated this week
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- Random Acceleration Molecular Dynamics in GROMACS☆34Updated 7 months ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆76Updated 8 months ago
- A fast solver for large scale MBAR/UWHAM equations☆38Updated 5 months ago
- Temperature generator for Replica Exchange MD simulations☆27Updated 2 years ago
- ☆26Updated 3 weeks ago
- 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 year
- A general small molecule force field descended from AMBER99 and parm@Frosst, available in the SMIRNOFF format☆28Updated 5 months ago
- ☆52Updated last year
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆65Updated last year
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆36Updated last year
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆30Updated last year
- ☆26Updated 8 months ago
- Bayesian Multistate Bennett Acceptance Ratio Method☆13Updated 2 months ago
- ☆48Updated 2 weeks ago
- A tool for setting up free energy simulations.☆35Updated 2 years ago