xray.Dynamics(1) Manual Page

Name

xray.Dynamics - Run Dynamics on an X-ray target.

Synopsis

xray.Dynamics [-AAhooSSUUV] [--nsf] [--nsf] [--rmo] [--rmo] [--aRadBuffer=0.75] [--aRadBuffer=0.75] [-b=Bussi] [-b=Bussi] [-B=1.0] [-B=1.0] [-d=1. _ 0_] [-d=1.0] [-F=XYZ] [--FSigFCutoff=-1.0] [--FSigFCutoff=-1.0] [-G=0.6] [-G=0.6] [-i=Verlet] [-i=Verlet] [-k=1.0] [-k=1.0] [-m=coordinates] [-m=coordinates] [--mdE=FFX] [--mdE=FFX] [-n=1000000] [-n=1000000] [--nBins=10] [--nBins=10] [--nResidueBFactor=0] [--nResidueBFactor=0] [-r=0.25] [-r=0.25] [-R=-1] [-R=-1] [--sigmaATol=0.05] [--sigmaATol=0.05] [--sol=POLYNOMIAL] [--sol=POLYNOMIAL] [-t=298.15] [-t=298.15] [-w=10.0] [-w=10.0] [--wA=1.0] [--xrayScaleTol=1.0e-4] [--xrayScaleTol=1.0e-4] [-z=100] [-z=100] [-X=<data> <data> <data>]… [-X=<data> <data> <data>]… files…

Description

Run Dynamics on an X-ray target.

Options

-F, --fileFormat=XYZ: Choose file type to write [PDB/XYZ].
-h, --help: Print command help and exit.
-V, --version: Print the Force Field X version and exit.
--wA, --dataWeight=1.0: The weight of the experimental data (wA).

X-ray Refinement Options

-m, --mode=coordinates: Refinement mode: coordinates, bfactors and/or occupancies.
--rmo, --refineMolOcc: Refine molecular occupancy.

X-ray Reflection Data Options

--FSigFCutoff=-1.0: F / SigF cutoff (-1.0 is no cutoff).
--nBins=10: The number of refection bins.
-R, --rFreeFlag=-1: R-Free Flag value (-1 attempts to auto-determine from the data).
-X, --data=<data> <data> <data>: Specify input data filename, its weight (wA) and if its from a neutron experiment (e.g. -X filename 1.0 false).

X-ray B-Factor Options

-B, --bSimWeight=1.0: B-Factor similarity weight.
--nResidueBFactor=0: Number of residues per B-factor. 0 uses atomic B-factors (default).
-U, --addAnisoU: Add Anisotropic B-Factors to refinement.

X-ray Target Options

-A, --allGaussians: Use all defined Gaussians for atomic scattering density (the default is to use the top 3).
--aRadBuffer=0.75: Scattering is evaluated within the atomic radius plus this buffer (Å).
-G, --sampling=0.6: The number of grid spaces per Angstrom for the scattering FFT grid.
--nsf, --noSplineFit: Use a resolution dependent spline scale factor.
--sigmaATol=0.05: Sigma A optimization tolerance.
--xrayScaleTol=1.0e-4: X-ray scale optimization tolerance.

X-ray Bulk Solvent Options

-S, --solventGridSearch: Perform a grid search for optimal bulk solvent parameters.
--sol, --solvent=POLYNOMIAL: Bulk solvent scattering model [Polynomial/Gaussian/Binary/None]

Dynamics Options

-b, --thermostat=Bussi: Thermostat: [Adiabatic / Berendsen / Bussi].
-d, --dt=1.0: Time discretization step in femtoseconds.
-i, --integrator=Verlet: Integrator: [Beeman / Respa / Stochastic / Verlet].
-k, --checkpoint=1.0: Interval in psec to write out restart files (.dyn, .his, etc).
--mdE, --molecularDynamicsEngine=FFX: Use FFX or OpenMM to integrate dynamics.
-n, --numberOfSteps=1000000: Number of molecular dynamics steps.
-o, --optimize: Optimize and save low-energy snapshots.
-r, --report=0.25: Interval in psec to report thermodynamics (psec).
-t, --temperature=298.15: Temperature (Kelvin).
-w, --write=10.0: Interval in psec to write out coordinates (psec).
-z, --trajSteps=100: Number of steps per MD cycle (--mdE = OpenMM only).

Arguments

files…: PDB and Diffraction input files.