Force Field Xxray.Dynamics(1)
Synopsis
xray.Dynamics [-AhoSUV] [--nsf] [--rmo] [--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…
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).