new-system

Pestifer provides a subcommand new-system as a convenient way to generate a bare-bones system configuration file for a new simulation. This is useful when you want to start a new simulation from scratch.

pestifer new-system accepts a single argument, which is intepreted as either the PDB ID or AlphaFold ID of the new system.

For example, to create a new system configuration file for the PDB ID 1abc, you would run:

$ pestifer new-system 1abc

This will create a new file named 1abc.yaml in the current directory, containing a basic configuration for the system that, by default, has only a fetch task and a single psfgen task:

title: New template pestifer input configuration for PDB ID 1abc
tasks:
  - fetch:
      sourceID: 1abc
  - psfgen:

Using this config is helpful in getting over the first hurdle of a new system, which is making sure pestifer can write a good, albeit minimal, psfgen script.

The new-system subcommand bases its output on the example file for example 1, the simple BPTI system .

There are several options to new-system:

--full

Including this flag option will add solvation, minimization, and equilibration tasks to the configuration file. For example:

$ pestifer new-system 1abc --full

This will create a new file named 1abc.yaml in the current directory, containing a more complete configuration for the system, including tasks for solvation, minimization, and equilibration.

--output <filename>

This option allows you to specify the name of the output file for the new system configuration. For example:

$ pestifer new-system 1abc --output my_custom_config.yaml

This will create a new file named my_custom_config.yaml in the current directory, containing the same configuration as 1abc.yaml, but with the specified filename.

--title <title>

This option allows you to specify a custom title for the new system configuration. For example:

$ pestifer new-system 1abc --title "My Custom Title"

This will create a new file named 1abc.yaml in the current directory with the specified title.