reweightingtools

python library to simulate via openmmtools extension with Girsanov path reweighting and to analyse with a reweighted MSM of deeptime

How to set up the reweighting software?

1. download existing software with reweighting modification

   a) go to github https://github.com/anyschaefer

   b) clone the modified openmmtools, deeptime package by

   • copying the "HTTPS clone URL" link that appears after selecting the code icon and
   • run git clone [url] in the directory you want to download it to

2. create new environment (RWGHTSoftware) with conda create -n RWGHTSoftware python=3.11 and install

   conda install -c anaconda matplotlib

   conda install -c anaconda spyder

   pip insatll . # in cloned deeptime path within deeptime folder

   pip insatll . # in cloned openmmtools path within openmmtools folder

   conda install -c conda-forge openmm

   conda install -c conda-forge mdtraj

   conda install -c conda-forge netcdf4

   conda install -c conda-forge mpiplus

   conda install -c omnia pymbar

   conda install -c numba numba

3. create scripts for simulation and analysis with Girsanov reweighting or use the setup and templates in reweightingtools