• 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
opc3box.pdb 44 KB