CREST and Trajectory Workflows

This page covers workflows for submitting Gaussian jobs from CREST conformer ensembles and MD trajectories, with optional pre-grouping to reduce redundant calculations.

Note

Behavior of -N parameter:

Without -g (no grouping): -N selects the N lowest-energy conformers directly.
With -g (grouping enabled): -N first groups conformers into N groups, then selects the lowest-energy conformer from each group as representative.

This means -g irmsd -N 10 gives 10 structurally diverse conformers, while -N 10 alone gives the 10 lowest-energy conformers (which may be similar).

CREST Workflow

The crest subcommand processes CREST conformer ensembles (multi-structure xyz files), optionally groups them, and generates Gaussian input files for each unique conformer.

Basic Usage

# Submit all conformers without grouping
chemsmart sub gaussian -f crest_conformers.xyz crest

# Group conformers first, then submit unique ones
chemsmart sub gaussian -f crest_conformers.xyz crest -g irmsd -N 10

# Use threshold-based grouping
chemsmart sub gaussian -f crest_conformers.xyz crest -g irmsd -T 0.3

Grouping Options

Use -g to specify grouping strategy before submission:

# iRMSD grouping (recommended for symmetric molecules)
chemsmart sub gaussian -f conformers.xyz crest -g irmsd -N 15

# TFD grouping (good for flexible molecules)
chemsmart sub gaussian -f conformers.xyz crest -g torsion -T 0.1

# Tanimoto similarity
chemsmart sub gaussian -f conformers.xyz crest -g tanimoto -T 0.9

Available strategies: rmsd, hrmsd, spyrmsd, irmsd, pymolrmsd, tanimoto, torsion, isomorphism, formula, connectivity, energy

Strategy-specific Options

Option	Description
`--inversion`	For iRMSD: auto/on/off (default: auto)
`-ft, --fingerprint-type`	For tanimoto: rdkit/morgan/maccs/usr/usrcat (default: rdkit)
`--use-weights/--no-use-weights`	For torsion: use torsion weights (default: True)
`--max-dev`	For torsion: equal/spec (default: equal)

Trajectory Workflow

The traj subcommand processes MD trajectory or optimization trajectory files, selecting structures from the end of the trajectory.

Basic Usage

# Use last 10% of trajectory (default)
chemsmart sub gaussian -f trajectory.xyz traj

# Use last 50% of trajectory
chemsmart sub gaussian -f trajectory.xyz traj -x 0.5

# Group selected structures before submission
chemsmart sub gaussian -f trajectory.xyz traj -x 0.3 -g spyrmsd -N 5

Trajectory Options

Option	Description
`-x, --proportion-structures-to-use`	Proportion of structures from end of trajectory (0.0 < x <= 1.0, default: 0.1)

Note: Original conformer indices are preserved in the output to track which trajectory frames were selected.

Common Options

Both crest and traj share these grouping options:

Practical Examples

Example 1: CREST Post-processing for DFT

Process CREST output, group to 15 conformers, and submit for DFT optimization:

chemsmart sub gaussian -f crest_conformers.xyz crest -g irmsd -N 15 -np 4

Example 2: Trajectory Analysis

Select last 30% of MD trajectory, group, and submit for single-point calculations:

chemsmart sub gaussian -f md_trajectory.xyz traj -x 0.3 -g tfd -T 0.5 --no-use-weights