fast.md_gen

fast.md_gen.gromax module

class fast.md_gen.gromax.Gromax(top_file, mdp_file, n_cpus=1, n_gpus=None, processing_obj=None, index_file=None, itp_files=None, submission_obj=None, max_warn=2, min_run=False, source_file=None, env_exports=None, **kwargs)

Bases: base

Gromacs wrapper for running md simulations or minimizing structures

Parameters

• top_file (str,) – Gromacs topology filename.

• mdp_file (str,) – Gromacs mdp file that specifies simulation parameters.

• n_cpus (int, default = 1,) – The number of cpus to use with the simulation.

• n_gpus (int, default = None,) – The number of gpus to use with the simulation. If None, will only use cpus.

• processing_obj (object, default = None,) – Object that when run will output commands for processing trajectory. Look at GromaxProcessing.

• index_file (str, default = None,) – Optionally supply an index file.

• itp_files (list, default = None,) – Optionally supply a list of itp files that go along with the topology file.

• submission_obj (object,) – Submission object used for running the simulation. Look into SlurmSub or OSSub.

• max_warn (int, default = 2,) – Maximum number of gromacs warnings to allow.

• min_run (bool, default = False,) – Is this a minimization run? Helps with output naming.

• source_file (str, default = None,) – The path to a gromacs GMXRC file to source before running simulations.

• env_exports (str, default=None,) – A list of commands to submit before running a job.

property class_name

property config

run(struct, output_dir=None, check_continue=True)

setup_run(struct, output_dir=None)

class fast.md_gen.gromax.GromaxProcessing(align_group=None, output_group=None, pbc='mol', ur='compact', index_file=None)

Bases: base

Generates gromacs commands for aligning a trajectory and determining output coordinates.

property class_name

property config

run()