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Published October 19, 2017 | Version 0.1.1
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MobleyLab/blues: Version 0.1.1

Authors/Creators

  • 1. @MobleyLab
  • 2. University of California, Irvine

Description

  • Adding extra propagation steps between lambda 0.2 -> 0.8 in the alchemical integrator
    • User parameter nprop = 5 (Default).
  • Zeroing masses of atoms outside the 5.0A distance (Default) of the ligand in the alchemical system.
    • Distance for freezing atoms is now a user parameter with freeze_distance
    • Added option to set selection center freeze_center Default: 'LIG'
    • Added option to include solvent freeze_solvent Default: 'HOH,NA,CL'
  • Switch print statements for logging module
  • Made input parameters for functions in the Simulation class explicit
    • Set default values but can pass the input parameters from the opt dictionary
  • New parameter write_move for the acceptRejectNCMC function
    • Setting write_move = True will write the accepted move to a PDB file.
  • Changed runNCMC() to run().
    • Avoids potential confusion with function simulateNCMC()
  • Simplified NCMC trajectory reporter
    • Replacedwrite_ncmc parameter with ncmc_traj
    • If a string is specified for (i.e. ncmc_traj = ncmc_output, it will write every NCMC step to a DCD file named ncmc_output.dcd
  • Added a function _getSimulationInfo() that will print out the simulation time information

Files

MobleyLab/blues-0.1.1.zip

Files (1.6 MB)

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Additional details

Related works

Is supplement to
https://github.com/MobleyLab/blues/tree/0.1.1 (URL)