OpenMMEnergies

Nifty tool for analyzing Force field energies using OpenMM. The main file, energy.py, will loop over any frames in a PDB file and print out its energy components. An .xyz file can be used instead, but the atoms in both the .pdb and .xyz files must align with eachother. If no topology file is provided, the program will use the default AMBER99 force field.

Usage

python3 energy.py [-h] -pdb PDB [-psf PSF] [-prm PRM] [-xyz XYZ] [-qcin QCIN] [-chg CHG] [-top TOP] [-xml XML] [-ipt IPT]

options:
  -h, --help  show this help message and exit
  -pdb PDB    PDB file to base the calcualtions off of
  -psf PSF    CHARMM PSF topology file
  -prm PRM    AMBER prmtop topology file
  -xyz XYZ    XYZ file of coordinate frames to loop over
  -qcin QCIN  Q-Chem input file with coordantes to use
  -chg CHG    Supplimental column of charges to use
  -top TOP    Gromacs topology file with force field info
  -xml XML    OpenMM Force Field XML file to use
  -ipt IPT    Input file with options to controll program behavior

Input File

The optional input file uses a Q-Chem format where each input section starts with $section and ends with $end. For example, the main options section , $rem, with their default values applied would look something like this:

$rem
  nonbonded_eda       False     ! energy decomposition analysis for nonbonded interactions
  optimize            False     ! optimize structure first; uses only the first frame of PDB coords
  print_eda           True      ! print energy decomposition
  print_forces        False     ! print forces too (not implimented yet)
  opt_mode            openmm    ! optimization mode: openmm or build_in BFGS solver
  opt_freeze_main     False     ! freeze main atoms (not drude particles)
  opt_freeze_drude    False     ! freeze drude particles
  density_chg         True      ! replace charges with point nuclei and Slater electron densities
  compute_forces:     0         ! also compute forces:
                                !     compute_forces = 0 will not compute forces
                                !     compute_forces = 1 will compute forces for main interactions (Bonds, Nonbonded, etc.)
                                !     compute_forces = 2 same as 1, plus the forces for nonbonded_eda energies
                                !     compute_forces = 3 compute forces for nonbonded_eda energies only (excluding 1-4 interactions)
$end

When forces are computed, a separate "energy_report" directory will be created in the current working directory that contains all of the forces and energies. For the force results, each frame is separated by a single empty line.

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