test.PhDynamics(1) Manual Page

Name

test.PhDynamics - Run constant pH dynamics on a system.

Synopsis

test.PhDynamics [-hooVxx] [--oMC] [--oMC] [--printRatioData] [--sort] [--aa=<selection>] [--aa=<selection>] [-b=Bussi] [-b=Bussi] [--coordinateSteps=100] [--cycles=5] [-d=1.0] [-d=1.0] [-e=0. _ 05_] [-e=0.05] [--esvLog=0.25 (psec)] [-F=XYZ] [-i=Verlet] [-i=Verlet] [--ia=<selection>] [--ia=<selection>] [--initDynamics=10000] [-k=1.0] [-k=1.0] [--mdE=FFX] [--mdE=FFX] [-n=1000000] [-n=1000000] [--pH=7.4] [--pHGaps=1] [-r=0.25] [-r=0.25] [--rs=100] [--rs=100] [-t=298.15] [-t=298. _ 15_] [--titrationSteps=10] [-w=10.0] [-w=10.0] [-z=100] [-z=100] files…

Description

Run constant pH dynamics on a system.

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).

Replica Exchange Options

-e, --exponent=0.05: Exponent to set the exponential temperature ladder.
--oMC, --oneMonteCarlo: Execute 1 Monte Carlo move for each temperature in each cycle
--rs, --replicaSteps=100: Number of steps for replica exchange.
-x, --repEx: Execute temperature replica exchange

Arguments

files…: XYZ or PDB input files.