Other options

Membrane normal

By default, gorder uses the z-axis as the membrane normal, assuming that the membrane is built in the xy-plane. If your membrane is built in a different plane, you can manually specify the membrane normal in the input YAML file:

membrane_normal: x

In this example, the membrane normal is oriented along the x-axis, meaning that the membrane is built in the yz-plane.

Min samples

By default, gorder calculates order parameters for all bonds for which it collects at least one sample. If you want to increase the number of required samples, you can specify the minimum number of samples manually in the input YAML file:

min_samples: 10000

In this example, at least 10,000 samples are required for the bond to have a valid order parameter. If the number of samples is lower than this value, the order parameter will be NaN.

Overwrite

By default, gorder does not overwrite output files. Before writing an output file (or creating an output directory for the ordermaps), any existing file (or directory) with the same name is backed up. You can change this behavior by specifying the overwrite option in the input YAML file:

overwrite: true

In this example, no backups will be created, and files will be overwritten directly.

You can also specify this option on the command line when calling gorder:

$ gorder INPUT_YAML --overwrite

Silent

By default, gorder writes a lot of information about the progress of the analysis to the terminal (standard output). If you prefer not to see any of this information, you can specify it in the input YAML file:

silent: true

In this example, gorder will not write anything to standard output. Output files will still be generated, and the analysis will proceed as normal. If an error occurs, information about the error will be written to standard error output.