Force Field XPhDynamics(1)
Synopsis
PhDynamics [-hoVx] [--oMC] [--printRatioData] [--sort] [--aa=<selection>] [-b=Bussi] [--coordinateSteps=100] [--cycles=5] [-d=1.0] [-e=0.05] [--esvLog=0.25 (psec)] [-F=XYZ] [-i=Verlet] [--ia=<selection>] [--initDynamics=10000] [-k=1.0] [--mdE=FFX] [-n=1000000] [--pH=7.4] [--pHGaps=1] [-r=0.25] [--rs=100] [-t=298.15] [--titrationSteps=10] [-w=10.0] [-z=100] files…
Options
- --coordinateSteps=100
- Number of steps done propagating coordinates only on GPU in one cycle
- --cycles, --OMMcycles=5
- Number of times to cycle between titrating protons on CPU and propagating coordinates only on GPU
- --esvLog, --titrationReport=0.25 (psec)
- Interval in psec to report ESV energy and lambdas when cycling between GPU and CPU.
- -F, --fileFormat=XYZ
- Choose file type to write [PDB/XYZ].
- -h, --help
- Print command help and exit.
- --initDynamics=10000
- Number of initialization steps to take before replica exchange windows start.
- --pH, --constantPH=7.4
- Constant pH value for molecular dynamics
- --pHGaps=1
- pH gap between replica exchange windows.
- --printRatioData
- Print out the protonation ratios from throughout the simulation at the end
- --sort
- Sort archive files by pH
- --titrationSteps=10
- Number of steps done titrating protons on CPU in one cycle
- -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).