1. Command-line interface (CLI)

sm_confgen provides two command-line interfaces (CLI), including prep_ConfGen, run_ConfGen and analyze_ConfGen. prep_ConfGen parameterizes your ligand and runs energy minimzation and equilibration at each specified temperature. run_ConfGen runs the TREMD simulation in GROMACS and analyze_ConfGen performs the analysis necessary to segment out the unique conformers which were sampled in the TREMD simulation.

1.1. CLI prep_ConfGen

::

usage: prep_ConfGen [-h] [-y YAML] [-o OUTPUT] [-m MAXWARN]

This code prepares a ConfGen TREMD simulation given necessary inputs.

options:

-h, --help

show this help message and exit

-y YAML, --yaml YAML

The input YAML file that contains REXEE parameters. (Default: params.yaml)

-o OUTPUT, --output OUTPUT

The output file for logging how replicas interact with each other. (Default: ConfGen_log.txt)

-m MAXWARN, --maxwarn MAXWARN

The maximum number of warnings in parameter specification to be ignored.

1.2. CLI run_ConfGen

::

usage: run_ConfGen [-h] [-y YAML] [-o OUTPUT] [-m MAXWARN]

This code runs a runs a set of TREMD simulations given necessary inputs.

options:

-h, --help

show this help message and exit

-y YAML, --yaml YAML

The input YAML file that contains REXEE parameters. (Default: params.yaml)

-o OUTPUT, --output OUTPUT

The output file for logging how replicas interact with each other. (Default: ConfGen_log.txt)

-m MAXWARN, --maxwarn MAXWARN

The maximum number of warnings in parameter specification to be ignored.

1.3. CLI analyze_ConfGen

::

usage: analyze_ConfGen [-h] [-y YAML] [-o OUTPUT] [-m MAXWARN]

This code analyzes the output from TREMD to generate conformers given necessary inputs.

options:

-h, --help

show this help message and exit

-y YAML, --yaml YAML

The input YAML file that contains REXEE parameters. (Default: params.yaml)

-o OUTPUT, --output OUTPUT

The output file for logging how replicas interact with each other. (Default: ConfGen_log.txt)

-m MAXWARN, --maxwarn MAXWARN

The maximum number of warnings in parameter specification to be ignored.

2. Input YAML parameters

• gmx_executable: (Required)

  This must be the executable for a non-MPI enabeled GROMACS for prep_ConfGen and nn MPI enabeled GROMACS for run_ConfGen. Either will work for analyze_ConfGen, but the non-MPI enabeled installation is recommended.

• input_structure(Required)

  The filename and path for the input structure for which you want to run analysis. We recommend sdf file format to ensure accurate parameterization.

• output_name(Required)

  The name prefix which will be applied to all output files.

• runtime_args(OptionalDefault=None)

  The arguments which will be passed to GROMACS during the gmx mdrun step.

• grompp_args(OptionalDefault=None)

  The arguments which will be passed to GROMACS during the gmx grompp step.

• temp_range(OptionalDefault=[300, 306, 311.08, 316.23, 321.45, 326.74, 332.10, 337.54, 343.05, 348.63, 354.29, 360.02, 365.84, 371.73, 377.71, 383.76, 389.90, 396.12, 402.43, 408.83, 415.31, 421.88, 428.55, 435.30, 442.14, 449.07, 450])

  The temperature for each temperature replica. Both the number of the value of the temperature for each replica can be changed. These values are generic and may not work well for all systems.

• nst_sim(OptionalDefault=None)

  The number of simulation steps to run for the production simulation. This number will be mul;tiplied by the time step to determine the simulation length. The default production simulation length is 100 ns.

• df(OptionalDefault=None)

  The time step to run at if a time step other than the 0.002 ps or 2 fs is desired.

• water_model(OptionalDefault=TIP3P)

  The water model used for the simulation. Only water models accepted by OpenFF Interchange can be input.

• replex_rate(OptionalDefault=1000)

  The rate for which exchanges will be attempted between adjacent temperature replicas. This rate is in units of time steps.

• conformer_threshold(OptionalDefault=1)

  The number of frames for which a confomer must be sampled in order to create a new conformer group.

• peak_threshold(OptionalDefault=0.0005)

  The proability minima which must be reached in order to differentiate a peak in the torsion proability distributions.

• min_probability(OptionalDefault=0.001)

  The minimum probabilty that a conformer must have in order to distingush a new conformer group.