Force Field Xrealspace.Anneal(1)
Synopsis
realspace.Anneal [-hoV] [--rv] [--aa=<selection>] [-b=Bussi] [-d=1.0] [-F=XYZ] [-i=Verlet] [--ia=<selection>] [-k=1.0] [--mdE=FFX] [-n=1000000] [-r=0.25] [-t=298.15] [--tl=10.0] [--tmA=0] [--tmB=0] [--tmS=EXP] [--tu=1000.0] [-w=10.0] [-W=10] [--wA=1. _ 0_] [-z=100] [-X=<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, --data=<data> <data>
- Specify input data filename and its weight (wA) (e.g. -X filename 1.0).
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.
Atom Selection Options
- --aa, --active=<selection>
- Ranges of active atoms [NONE, ALL, Range(s): 1-3,6-N].
- --ia, --inactive=<selection>
- Ranges of inactive atoms [NONE, ALL, Range(s): 1-3,6-N].
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).