CCPBioSim / fesetupLinks
A tool for setting up free energy simulations.
☆36Updated 2 years ago
Alternatives and similar repositories for fesetup
Users that are interested in fesetup are comparing it to the libraries listed below
Sorting:
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆72Updated 2 years ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆49Updated 4 years ago
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆79Updated 2 years ago
- OpenMM plugin to interface with PLUMED☆68Updated 7 months ago
- ☆65Updated 2 months ago
- A python implementation of the string method with swarms of trajectories using GROMACS☆18Updated 2 years ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆60Updated last year
- An Open-Source Molecular Builder and Free Energy Preparation Workflow☆129Updated last month
- Benchmark set for relative free energy calculations.☆116Updated last year
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆33Updated 3 months ago
- A repository containing the build steps for the ccpbiosim workshop on QM/MM☆67Updated this week
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆84Updated 2 months ago
- Analysis of non-covalent interactions in MD trajectories☆63Updated 9 months ago
- ☆67Updated 2 years ago
- Python code for generating Boresch restraints from MD simulations☆22Updated 3 years ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆67Updated 2 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆18Updated 2 years ago
- Set up relative free energy calculations using a common scaffold☆24Updated last month
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated 2 years ago
- Martini 3 small molecule database☆65Updated last month
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆44Updated 4 years ago
- MDANCE is a flexible n-ary clustering package for all applications.☆79Updated this week
- The public versio☆65Updated 2 years ago
- binding free energy estimator 2☆128Updated this week
- ☆53Updated 3 months ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago
- Random Acceleration Molecular Dynamics in GROMACS☆39Updated last year
- Temperature generator for Replica Exchange MD simulations☆29Updated 2 years ago
- Python tutorial for estimating and clustering free energy landscapes with InfleCS.☆30Updated 3 years ago