Conformational Sampling & Dynamics (Gaussian)

This page covers CREST conformational searches and trajectory analysis using Gaussian.

CREST Jobs

CREST (Conformer-Rotamer Ensemble Sampling Tool) performs systematic conformational searches to find low-energy conformers. CHEMSMART combines CREST with Gaussian for subsequent calculations.

chemsmart sub [OPTIONS] gaussian [GAUSSIAN_OPTIONS] crest -j <jobtype> [SUBCMD_OPTIONS]

CREST Options

Option	Type	Description
`-j, --jobtype`	string	Job type: opt, ts, modred, scan, sp (required)
`-nc, --num-confs-to-run`	int	Number of conformers to process

Warning

The -j, --jobtype option is required for CREST jobs.

Basic Usage

Run optimization on CREST conformers:

chemsmart sub gaussian -p project -f crest_conformers.xyz -c 1 -m 1 crest -j opt

Run TS optimization on conformers:

chemsmart sub gaussian -p project -f crest_conformers.xyz -c 0 -m 1 crest -j ts

Run modred optimization with constraints:

chemsmart sub gaussian -p project -f crest_conformers.xyz -c 0 -m 2 crest -j modred -c [1,4]

Note

The <input_file> is typically the CREST output file named crest_conformers.xyz.

Examples

Process 10 lowest-energy conformers:

chemsmart sub gaussian -p project -f crest_conformers.xyz -l structure_from_lowest -c 0 -m 1 crest -j opt -nc 10

Output files are named structure_from_lowest_opt_c1 through structure_from_lowest_opt_c10.

Note

If a job terminates before all conformers are processed (e.g., walltime limit), resubmitting will continue from where it left off.

Trajectory Analysis

Process molecular dynamics trajectories and extract structures for further analysis:

chemsmart sub [OPTIONS] gaussian [GAUSSIAN_OPTIONS] traj -j <jobtype> [SUBCMD_OPTIONS]

Trajectory Options

Option	Type	Description
`-j, --jobtype`	string	Job type: opt, ts, modred, scan, sp (required)
`-ns, --num-structures-to-run`	int	Number of structures from the end of trajectory to process
`-x, --proportion-structures-to-use`	float	Proportion of trajectory to use (0.0 < x <= 1.0, default: 0.1) At least one structure is always selected.

Warning

The -j, --jobtype option is required for trajectory analysis.

Basic Usage

Process trajectory structures:

chemsmart sub gaussian -p project -f trajectory.xyz -c 0 -m 1 traj -j opt

Use the last 30% of trajectory:

chemsmart sub gaussian -p project -f md.traj -c 0 -m 1 traj -j opt -x 0.3

Grouper Options for CREST/Trajectory Jobs

Please check

CREST and Trajectory Workflows

for more details about this workflow.