/Funnel-metadynamics

This repo is designed to give initial files to perform Funnel metadynamics as described in the paper Resolving the problem of trapped water in binding cavities: prediction of host–guest binding free energies in the SAMPL5 challenge by funnel metadynamics (https://link.springer.com/article/10.1007/s10822-016-9948-6)

Primary LanguagePython

Funnel-metadynamics-SAMPL5

This repo is designed to give initial files to perform Funnel metadynamics as described in the paper Resolving the problem of trapped water in binding cavities: prediction of host–guest binding free energies in the SAMPL5 challenge by funnel metadynamics (https://link.springer.com/article/10.1007/s10822-016-9948-6)

This repo is mainly compatible with Plumed 1.3 (request: will be great if someone wants to make a Plumed 2.6 compatible version of this repo)

  1. Inside Create funnel folder you will find a .py file which will produce a funnel restraint using user defined variables and will outpout a .dat file. which can be used with Plumed 1.3

  2. The folder 1D funnel metadynamics contains example inputs to run funnel metadynamics for host-guest system.