1. 28 Jun, 2022 1 commit
    • Alex Izvorski's avatar
      OPC and OPC3 water (#3654) · 583471a6
      Alex Izvorski authored
      * Add benchmarks from Amber20 benchmark suite to standard benchmark script
      
      * Add ensemble option; don't change hydrogen mass in amber input files
      
      * Download and extract .tar.gz using pure python code, no wget/tar dependencies
      
      * Rename amber tests
      
      * add opc and opc3 models
      
      * update to match https://bioinformatics.cs.vt.edu/~izadi/OPC_Gromacs/opc.top
      
      
      
      * opc box, converted from ambertools-22.0-py38h6177452_1/dat/leap/lib/opcbox.off
      
      * change values to make serialized system match one created from prmtop as close as possible
      
      * unit test for opc water
      
      * opc - final values, match frcmod.opc; derivation in comments
      
      * opc3 water - final values, shows derivation
      
      * opc3box made from ambertools 22 dat/leap/lib/opc3box.off
      
      * add opc3 water test
      
      * add opc and opc3 to docs
      
      * move tests to TestForceField.py
      
      * move opc tests out of amoeba tests, oops
      
      * move opcbox and opc3box pdb files
      Co-authored-by: default avatarAlex Izvorski <alex@genesistherapeutics.ai>
      583471a6