Create Custom Torsion Rules¶

This Cube generates custom torsion rules which can be used with the Psi4 Conformer Generation Cube based on torsion scans of fragments around each molecule’s rotatable bonds

Main Parameters¶

Parameter Name	Associated Port	Port Type
Conformer Angle Field
atom tag
Conformer Energy Field

Parameter Details¶

Calculation Parameters
Field parameters
Hardware Parameters
Metrics Parameters

Calculation Parameters¶

atom tag (string) : Tag for the atoms in torsion

CPUs (integer) : The number of CPUs to run this cube with

Default: 1 Min: 1 Max: 128

Cube Metrics (string) : Set of metrics to be collected

Choices: cpu, disk, memory, network

Temporary Disk Space (MiB) (decimal) : The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.

Default: 5120.0 Min: 128.0 Max: 8589934592

GPUs (integer) : The number of GPUs to run this cube with

Default: 0 Max: 16

Instance Tags (string) : Only run on machines with matching tags (comma separated)

Default: “”

Instance Type (string) : The type of instance that this cube needs to be run on

Angle Step Size (decimal) : Chose the maximum step size for sampling around local minima.

Default: 30 Min: 0.1 Max: 180

How many points to sample around minima (integer) : Chose the number of points to sample aboveand below local minima. Recommended values are 1-3

Default: 180 Min: 1 Max: 180

Energy Cutoff (decimal) : Energy cutoff for choosing angles in custom torsion rules. Default value of 5kcal is chosen based on the assumption that these rules will later be used to generate conformers in a 10kcal/mol energy window. If you plan to generate a QM conformer ensemble in a larger energy window you may want to increase this cut off accordingly.

Default: 5 Min: 0.1

Memory (MiB) (decimal) : The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.

Default: 1800 Min: 256.0 Max: 8589934592

Metric Period (decimal) : How often to sample metrics, in seconds

Default: 60 Min: 1 Max: 300

Spot policy (string) : Control cube placement on spot market instances

Default: Prohibited

Choices: Allowed, Preferred, NotPreferred, Prohibited, Required

Field parameters¶

Conformer Angle Field (Field Type: Float) :

Default: Torsion angle

Conformer Energy Field (Field Type: Float) :

Default: Psi4 Energy (kcal/mol)

Extended Log Field (Field Type: StringVec) : Message extended log field

Default: Extended Log Field

Input Molecule Field (Field Type: Chem.Mol) : Primary Molecule Field to use as input to the Cube

Log Field (Field Type: String) : Message log field

Default: Log Field

Output Molecule Field (Field Type: Chem.Mol) : Primary Molecule Field to use as output to the Cube

Fragment Parent Molecule Field (Field Type: Chem.Mol) : Field for storing parent molecule with torsion atoms tagged.

Default: Fragment Parent Molecule

Conformer Strain Energy Field (Field Type: Float) :

Default: Psi4 Strain Energy (kcal/mol)

Conformer Angle After Optimization (Field Type: Float) :

Default: Updated Torsion Angle

Hardware Parameters¶

Machine hardware requirements