Synopsis

realspace.Dynamics [-hoV] [--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] [-w=10.0] [--wA=1.0] [-z=100] [-X=<data> <data>]…​ files…​

Description

Molecular dynamics on a Real Space target.

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).

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).

Arguments

files…​

PDB and Real Space input files.