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Dynamics(1) Manual Page


Dynamics - Run dynamics on a system.


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


Run dynamics on a system.


-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



XYZ or PDB input file.