Simulated Annealing
Run molecular dynamics at a series of temperatures to optimize a structure.
Usage: ffxc Anneal [-ho] [--tl=10.0] [--tu=1000.0] [-b=Bussi] [-d=1.0] [-i=Verlet] [-k=1.0] [-n=1000000] [-r=0.25] [-t=298.15] [-w=10.0] [-W=10] files...
Run simulated annealing on a system.
files... XYZ or PDB input files.
--tl, --temperatureLow=10.0 Low temperature limit (Kelvin).
--tu, --temperatureUpper=1000.0 High temperature limit (Kelvin).
-b, --thermostat=Bussi Thermostat: [Adiabatic / Berendsen / Bussi].
-d, --dt=1.0 Time discretization step in femtoseconds.
-h, --help Print this help message.
-i, --integrator=Verlet Integrator: [Beeman / Respa / Stochastic / Verlet].
-k, --checkpoint=1.0 Interval to write out restart files (.dyn, .his, etc).
-n, --numberOfSteps=1000000 Number of molecular dynamics steps.
-o, --optimize Optimize and save low-energy snapshots.
-r, --report=0.25 Interval to report thermodynamics (psec).
-t, --temperature=298.15 Temperature (Kelvin).
-w, --write=10.0 Interval to write out coordinates (psec).
-W, --windows=10 Number of annealing windows.