{"repo":"rinikerlab/reeds","free":true,"listed":false,"github":"https://github.com/rinikerlab/reeds","clone":"git clone https://github.com/rinikerlab/reeds.git","description":"This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.","language":"Python","stars":34,"topics":["drug-design","free-energy-calculations","gromos","python","hpc","replica-exchange","enhanced-sampling","eds","workflow"],"license":"MIT","category":"workflow-automation","readme_excerpt":"REEDS ============================== [//]: # (Badges) Replica Exchange - Enveloping Distribution Sampling (RE-EDS) is a method to calculate the relative free energy of multiple states in a system. It can be applied to calculate relative solvation free energies or relative binding free energies with Gromos. One advantage of this method is that no alchemical transition path from one end state to another end state is required thanks to Enveloping Distribution Sampling (EDS) by Christ et al. . EDS allows to explore the end state graph during the simulation with multiple different alchemical transition paths. The enhanced sampling method Replica Exchange was added by Sidler et al. to speed up the sampling and ease the choice of parameters. Additionally, multiple modules were described by Sidler to allow an automatization of the pipeline. In this repository, we now combined these approaches to an automatic scheme for RE-EDS. The repository aims to make the RE-EDS pipeline accessible to everyone! For more on RE-EDS checkout: Leveraging the sampling efficiency of RE-EDS in OpenMM using a shifted reaction-field with an atom-based cutoff; Salomé R. Rieder, Benjamin Ries, Alžbeta Kubincová, Candide Champion, Emilia P. Barros, Philippe H. Hünenberger, and Sereina Riniker (2022). Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules; Salomé R. Rieder, Benjamin","default_branch":null,"files":null,"tree":[],"storefront":"/r/rinikerlab","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/rinikerlab/reeds/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}