General parameters

These are general parameters that affect the global behaviour of the Platform.

List of general parameters:

List of examples:

cpus

  • Description: The number of computation cores that the Platform will use.

  • Type: Integer

  • Default: 60

Note

When running on test mode the number of cpus is ignored and the simulation only uses 5 of them.

See also

test, Example 1, Example 2, Example 3

test

  • Description: Run a quick test to check the simulation works (~2 min).

  • Type: Boolean

  • Default: False

Warning

Never use the control files generated in test mode as input for a production simulation because other parameters such as temperature, ANM and minimization are tweaked to make simulation faster.

See also

cpus, Example 1, Example 2

debug

  • Description: Use this flag to only create the inputs of the simulation. No actual simulation will run.

  • Type: Boolean

  • Default: False

Note

The combination of this parameter along with debug allows the user to manually modify any input file that the Platform generates. For example, running first in debug mode will generate input files like pele.conf, adaptive.conf or ligand templates. The user can then modify them at their will and restart the job with restart.

See also

restart, Example 1

restart

  • Description: Use restart parameter set to True to start a simulation from scratch (with existing input PDBs and configuration files).

  • Type: Boolean

  • Default: False

Note

The combination of this parameter along with debug allows the user to manually modify any input file that the Platform generates. For example, running first on debug mode will generate input files like pele.conf, adaptive.conf or ligand templates. The user can then modify them at their will and restart the job with restart.

Note

This parameter must not be confused with adaptive_restart. While restart stands for skipping any input file preparation and directly going to the simulation execution, it still can start from the first Adaptive iteration if adaptive_restart is set to False.

See also

debug, adaptive_restart, Example 1, Example 3

seed

  • Description: Seed for Platform’s pseudo-random numbers generator for reproducibility. When no seed is set, it will be initialized to a random number. This random number can be consulted afterwards by checking adaptive.conf file.

  • Type: Integer

  • Default: None

Note

It is always a good practice to establish a fixed seed in order to guarantee reproducibility.

See also

Example 1

working_folder

  • Description: Directory where the simulation will run.

  • Type: String

  • Default: LIG_Pele, where LIG is the residue name of our ligand

Note

When working_folder is not set, the default behaviour is to never replace an existing folder. So, in case that LIG_Pele directory already exists, the ultimate working_folder will be set to LIG_Pele_1, LIG_Pele_2, and so on.

See also

Example 1, Example 3

Example 1

In this example we set an induced fit docking simulation with 10 computation cores and run it in debug mode. Moreover, test and restart modes are disabled. Finally, we also establish a specific seed for the pseudo-random numbers generator and a custom working folder.

# General parameters
cpus: 10
test: False
debug: True
restart: False
seed: 2021
working_folder: "my_custom_choice"

# Required parameters
system: 'system.pdb'
chain: 'L'
resname: 'LIG'

# Package selection
induced_fit_fast: True

Example 2

In this example we set an induced fit docking simulation with 10 computation cores and run it in test mode. When using this mode, the number of computation cores that will be used is always going to be 5, regardless of the number of cores requested with the cpus parameter.

# General parameters
cpus: 10
test: True

# Required parameters
system: 'system.pdb'
chain: 'L'
resname: 'LIG'

# Package selection
induced_fit_fast: True

Example 3

In this example we ask the induced fit docking simulation to be restarted. Consequently, the Platform expects to find a directory previously created with valid input files. To generate them, we need to execute the Platform in debug mode, as shown in Example 1. So, in this case the working_folder that we set it must already exist.

# General parameters
cpus: 10
restart: True
working_folder: "my_custom_choice"

# Required parameters
system: 'system.pdb'
chain: 'L'
resname: 'LIG'

# Package selection
induced_fit_fast: True