Molecular dynamics on a Real Space target.
realspace.Dynamics(1) Manual Page
Name
realspace.Dynamics - Molecular dynamics on a Real Space target.
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
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.