Conformational Search (CREST)

This page covers conformational sampling workflows using CREST (Conformer-Rotamer Ensemble Sampling Tool).

For a complete list of CLI options, see CREST CLI Options.

Free Conformational Search

Sample the conformational landscape of a molecule using CREST.

chemsmart sub [OPTIONS] crest [CREST_OPTIONS] conformers

Basic Usage

Standard conformational search:

chemsmart sub -s server crest -p project -f struct.xyz -c 0 -m 1 conformers

Constrained Conformational Search

Sample conformations while maintaining fixed geometric constraints (distance, angle, or dihedral). This is useful for transition state conformer searches or other applications where certain geometric parameters must be held constant.

chemsmart sub [OPTIONS] crest [CREST_OPTIONS] conformers [SUBCMD_OPTIONS]

Constrained Search Options

Option	Type	Description
`-c, --constraints`	string	Coordinates to constrain (1-indexed). Distance `[i,j]`, angle `[i,j,k]`, dihedral `[i,j,k,l]`. Example: `[[1,2],[5,7,8],[3,4,1,7]]`
`-f, --force-constant`	float	Harmonic restraint force constant in Hartree/Bohr².

Basic Usage

Constrained search:

chemsmart sub -s server crest -p project -f molecule.log conformers \
   --constraints [[1,2],[5,7,8],[3,4,1,7]]

With explicit force constant:

chemsmart sub -s server crest -p project -f molecule.log conformers \
  --constraints [[1,2],[2,3]] \
  --force-constant 0.25

How Constraints Work

When you specify --constraints, CHEMSMART:

Reads the input geometry and measures the requested distances, angles, and/or dihedrals
Generates a constraints.inp file (xTB xcontrol $constrain syntax) with those values and an optional force constant
Passes this to CREST via --cinp constraints.inp

Example generated constraints.inp:

$constrain
   force constant=0.25
   distance: 1, 2, 1.4923
   angle: 5, 7, 8, 109.4712
   dihedral: 3, 4, 1, 7, 180.0000
$end

Output Layout

After a successful CREST run, the output directory typically includes:

File	Description
`crest_conformers.xyz`	Conformer ensemble, sorted by energy
`crest_best.xyz`	Lowest-energy conformer, typically used for subsequent calculations.
`crest_rotamers.xyz`	Rotamer ensemble
`crest.energies`	Relative energy values for all conformers (in kcal/mol)
`{label}.out`	Main CREST log output with sampling details
`constraints.inp`	Constraint file (only for constrained searches)

The generated conformers can be visualized or reused as input for subsequent calculations (e.g. -f path/to/crest_conformers.xyz).

Next Steps

CREST CLI Options — Full CLI option reference
CREST and Trajectory Workflows — Process conformer ensembles
Conformational Sampling & Dynamics (Gaussian) — Run Gaussian calculations on conformers
Basic Visualization (PyMOL) — visualize CREST conformer or rotamer ensembles