Dynamics(1) Manual Page

Name

Dynamics - Run dynamics on a system.

Synopsis

Dynamics [-hooVxx] [--iso] [--iso] [--oMC] [--oMC] [--aa=<selection>] [--aa=<selection>] [-b=Bussi] [-b=Bussi] [--barInt=10] [--barInt=10] [--bpi=1000] [--bpi=1000] [-d=1.0] [-d=1.0] [-e=0.05] [-e=0.05] [-F=XYZ] [-i=Verlet] [-i=Verlet] [--ia=<selection>] [--ia=<selection>] [-k=1.0] [-k=1.0] [--maxAM=0.5] [--maxAM=0.5] [--maxD=1.6] [--maxD=1. _ 6_] [--maxV=1.0] [--maxV=1.0] [--mdE=FFX] [--mdE=FFX] [--minD=0.75] [--minD=0.75] [-n=1000000] [-n=1000000] [-p=0] [-p=0] [-r=0.25] [-r=0. _ 25_] [--rs=100] [--rs=100] [-t=298.15] [-t=298.15] [-w=10.0] [-w=10.0] [-z=100] [-z=100] file

Description

Run dynamics on a system.

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).

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

file: XYZ or PDB input file.