test.PhBar(1) Manual Page

Name

test.PhBar - Use the BAR algorithm to estimate a free energy difference for a CpHMD system.

Synopsis

test.PhBar [-hoV] [-b=Bussi] [--coordinateSteps=10000] [-d=1.0] [-F=XYZ] [-i=Verlet] [--iterations=999] [-k=1.0] [--mdE=FFX] [-n=1000000] [--pH=7.4] [-r=0.25] [-t=298.15] [--tautomerFix=0] [--titrationFix=0] [-w=10.0] [-z=100] files…

Description

Use the BAR algorithm to estimate a free energy difference for a CpHMD system.

Options

--coordinateSteps=10000: Number of steps done on GPU before each evaluation
-F, --fileFormat=XYZ: Choose file type to write [PDB/XYZ].
-h, --help: Print command help and exit.
--iterations=999: Number of times to evaluate neighbor energies
--pH, --constantPH=7.4: Constant pH value for molecular dynamics windows
--tautomerFix=0: Constant tautomer value for molecular dynamics windows
--titrationFix=0: Constant titration value for molecular dynamics windows
-V, --version: Print the Force Field X version and exit.

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…: XYZ or PDB input files.