cspy-flex command

The cspy-flex command is used to perform crystal structure prediction calculations for flexible molecules. Molecules are treated as rigid during geometry optimisation but molecules have different conformations at the point of random structure generation.

cspy-flex [-h] [-c CHARGES] [-m MULTIPOLES] [-a AXIS] [-g SPACEGROUPS] [-n NUMBER_STRUCTURES]
          [--nudge NUDGE] [--adaptcell] [--asi] [--clg-chomp CLG_CHOMP | --clg-aut]
          [-p {fit,fit_disponly,fit_reponly,w99,fit_water_X,Day_halobenzenes,w99_orig_Halogens,w99_orig_H,w99rev_6311,w99rev_6311_s,w99rev_631,w99rev_pcm_6311,w99_s_cl,w99sp,w99rev_pcm_6311_and_Chloride,w99rev_pcm_6311_and_Bromide,w99rev_pcm_6311_and_Iodide,w99rev_pcm_6311_and_Halides,isoPAHAP,PAHAP,nothing,gaff2_LJ,gaff2_fit}]
          [--cutoff CUTOFF] [--conf_energy_window CONF_ENERGY_WINDOW] [--log-level LOG_LEVEL]
          [--keep-files] [--skip-header] [--status-file STATUS_FILE]
          databases [databases ...]

positional arguments

  • databases - Databases containing molecular conformations with multipoles generated from cspy-moldis

options

  • -h, --help - show this help message and exit

  • -c CHARGES, --charges CHARGES - Rank0 multipole file

  • -m MULTIPOLES, --multipoles MULTIPOLES - RankN multipole file

  • -a AXIS, --axis AXIS - Axis filename for structure minimization

  • -g SPACEGROUPS, --spacegroups SPACEGROUPS - Spacegroup set for structure generation (default: fine10)

  • -n NUMBER_STRUCTURES, --number-structures NUMBER_STRUCTURES - Number of structures for structure generation

  • --nudge NUDGE - Nudge molecules in assymetric unit that fail QR step (default: 0)

  • --adaptcell - Adaptively optimise cell parameters

  • --asi - Allow molecules to have superimposed centroids (set to true for encapsulation)

  • --clg-chomp CLG_CHOMP - Use the chomp CLG with molecular pairs from the provided database

  • --clg-aut - Use the AUT CLG with molecular pairs. If not running a CSP, a database must exist of format: [seed]-spacegroup-AU.db

  • -p POTENTIAL, --potential POTENTIAL - intermolecular potential name (default: fit)

  • --cutoff CUTOFF - dmacrys real space/repulsion-dispersion cutoff (default: calculate)

  • --conf_energy_window CONF_ENERGY_WINDOW -

    When selecting conformers to generate crystals, the conf_energy_window defines the

    energy window above the minimum energy conformation from within which a conformation may be randomly selected.

    (default: 22.0)

  • --log-level LOG_LEVEL - Log level (default: INFO)

  • --keep-files - Keep DMACRYS and NEIGHCRYS files which, for each structure, are stored in a new directory in the pwd.

  • --skip-header - Skip the mol-CSPy header at the start of the job.

  • --status-file STATUS_FILE - Specify output status file (default: status.txt)

To use this app, there is one prerequisite:

  1. Generate a conformational database with cspy-moldis. See cspy-moldis command.

Workflow

The workflow for cspy-flex is almost identical to cspy-csp (see cspy-csp command) but differs slightly in use and in operation. cspy-csp generates random crystal structures comprised of molecules with a geometry defined by an input .xyz file. In cspy-flex, instead of sourcing molecular geometries from .xyz files, a conformation is selected randomly from a conformational database. The conformation’s corresponding _rank0.dma, .dma and .mols files for DMACRYS geometry optimisations are sourced automatically from the same database.

Command line usage of cspy-flex

Running a local cspy-flex calculation differs from cspy-csp in that instead of providing a list of .xyz files, a list of conformational database files should be provided instead. Additionally, there is no need to specify charge (-c), multipole (-m), or axes (-a) files. One new flag is introduced: --conf_energy_window. This conformational energy window enforces a maximum intramolecular energy above the lowest energy conformation. Conformers with relative energies greater than this value will not be included at the structure generation step. A default value is set in cspy.configuration.py but is 22 kJ/mol at the time of writing.

An example usage of cspy-flex is as below:

mpiexec -np 4 cspy-flex conformations.db --conf_energy_window 30 -g 33 -n 100