5. Command line arguments

Certain options are provided to HyMD as command line arguments. Besides input and output file specifications, these options mostly constitute debugging options such as disabling all bonded or particle–field interactions.

5.1. Required arguments

configuration file:

type positional

Specifies the .toml format configuration file containing simulation details. See Configuration file for details.

structure and topology file:

type positional

Specifies the positions, indices, names (and optionally molecular affiliation, bond structure, velocities). See Topology and structure file for details.

5.2. Optional arguments

-v  --verbose

type optional

Number of following arguments: 0 or 1

Determines the verbosity of the simulation logger. More verbose means more text output during runs. Verbosity may be increased by specifying -v or --verbose with no additional specification. This increases verbosity level by 1. Alternatively, it maye be specified by --verbose V with V being 0, 1, or 2.

--profile

type optional

Number of following arguments: 0

Enables code profiling using cProfile. This will output one profiling file per MPI rank invoked in the simulation.

--double-precision

type optional

Number of following arguments: 0

Specify usage of double precision internally in HyMD (including in the FFTs).

--double-output

type optional

Number of following arguments: 0

Specify usage of double precision in the output trajectory from HyMD.

--velocity-output

type optional

Number of following arguments: 0

Specify that velocities should be output to the HyMD trajectory.

--force-output

type optional

Number of following arguments: 0

Specify that forces should be output to the HyMD trajectory.

--disable-mpio

type optional

Number of following arguments: 0

Specify that a non-MPI-enabled HDF5 library is to be used, foregoing the parallel file IO capabilities of h5py. This is normally used as a compatibility option for machines on which installing MPI-enabled HDF5 is difficult.

--logfile

type optional

Number of following arguments: 1

Specifies the path of a plain text log file in which stdout is mirrored during simulation runs.

--seed

type optional

Number of following arguments: 1

Specifies the random seed used in the numpy random library to generate velocities, thermostatting, etc.

--disable-bonds

type optional

Number of following arguments: 0

Disable any two-particle bonds present in the system.

--disable-angle-bonds

type optional

Number of following arguments: 0

Disable any three-particle bonds present in the system.

--disable-dihedrals

type optional

Number of following arguments: 0

Disable any four-particle bonds present in the system.

--disable-dipole

type optional

Number of following arguments: 0

Disable any topological reconstruction of peptide backbone dipoles present in the system.

--disable-field

type optional

Number of following arguments: 0

Disable any particle–field interactions present in the system.