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xray.Dynamics(1) Manual Page


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


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


Run Dynamics on an X-ray target.


-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 on molecules.

X-ray Reflection Data Options


F / SigF cutoff (-1.0 is no cutoff).


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.


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).


Set the distance beyond the atomic radius to evaluate scattering (A).

-G, --sampling=0.6

The number of grid spaces per Angstrom for the scattering FFT grid.

--sf, --splineFit

Use a resolution dependent spline scale.


Sigma A optimization tolerance.


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).



PDB and Diffraction input files.