Simulated annealing on an X-ray target.
xray.Anneal(1) Manual Page
Name
xray.Anneal - Simulated annealing on an X-ray target.
Synopsis
xray.Anneal [-AhoSUV] [--rmo] [--rv] [--sf] [--aRadBuffer=0.75] [-b=Bussi] [-B=1.0] [-d=1.0] [--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] [--tl=10.0] [--tmA=0] [--tmB=0] [--tmS=EXP] [--tu=1000.0] [-w=10.0] [-W=10] [--wA=1.0] [--xrayScaleTol=1.0e-4] [-z=100] [-X=<data> <data> <data>]… files…
Description
Options
- -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
- --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
-
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.
- --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).
Simulated Annealing Options
- --rv, --reinitVelocities
-
Re-initialize velocities before each round of annealing.
- --tl, --temperatureLow=10.0
-
Low temperature limit (Kelvin).
- --tmA, --temperingAfter=0
-
Number of (annealing, not MD/MC) steps to remain at the low temperature
- --tmB, --temperingBefore=0
-
Number of (annealing, not MD/MC) steps to remain at the high temperature
- --tmS, --temperingSchedule=EXP
-
Tempering schedule: choose between EXP (exponential) or LINEAR
- --tu, --temperatureUpper=1000.0
-
High temperature limit (Kelvin).
- -W, --windows=10
-
Number of annealing windows.
Arguments
- files…
-
PDB and Diffraction input files.