Force Field XDynamics(1)
Synopsis
Dynamics [-hoVx] [--iso] [--oMC] [--aa=<selection>] [-b=Bussi] [--barInt=10] [--bpi=1000] [-d=1.0] [-e=0.05] [-F=XYZ] [-i=Verlet] [--ia=<selection>] [-k=1.0] [--maxAM=0.5] [--maxD=1.6] [--maxV=1.0] [--mdE=FFX] [--minD=0.75] [-n=1000000] [-p=0] [-r=0.25] [--rs=100] [-t=298.15] [-w=10.0] [-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).
Monte Carlo Pressure Options
- --barInt, --meanBarostatInterval=10
- Sets the mean number of MD steps between barostat move proposals.
- --bpi, --barostatPrintInterval=1000
- Sets the number of Barostat MC cycles between print statements.
- --iso, --isotropic
- Restrict the MC Barostat to isotropic moves.
- --maxAM, --maxAngleMove=0.5
- Sets the width of proposed crystal angle moves (uniformly distributed) in degrees.
- --maxD, --maxDensity=1.6
- Specify the maximum density accepted by the MC Barostat (g/cc).
- --maxV, --maxVolumeMove=1.0
- Default width of proposed unit cell side length moves (uniformly distributed) in Angstroms.
- --minD, --minDensity=0.75
- Specify the minimum density accepted by the MC Barostat (g/cc).
- -p, --npt=0
- Specify use of a MC Barostat at the given pressure; the default 0 disables NPT (atm).