Force Field XAnneal(1)
Synopsis
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] [-z=100] file
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.
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).
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.