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Real Space Annealing

Simulated annealing on a Real Space target.


Usage: ffxc realspace.Anneal [-ho] [--tl=10.0] [--tu=1000.0] [--wA=1.0] [-b=Bussi] [-d=1.0] [-i=Verlet] [-k=1.0] [-n=1000000] [-r=0.25] [-t=298.15] [-w=10.0] [-W=10] [-X=<data> <data>]... files...
Simulated annealing on a Real Space target.
    files...                            PDB and Real Space input files.
    --tl, --temperatureLow=10.0         Low temperature limit (Kelvin).
    --tu, --temperatureUpper=1000.0     High temperature limit (Kelvin).
    --wA, --dataWeight=1.0              The weight of the real space data (wA).
-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.
-X, --data=<data> <data>                Specify input data filename, and its weight (wA) (e.g. -X filename 1.0).