pyxtal.interface.charmm module

class pyxtal.interface.charmm.CHARMM(struc, label='_', algo='abnr', lat_mut=False, rotate=False, prefix='pyxtal', atom_info=None, folder='.', opt='conp', steps=None, exe='charmm', input='charmm.in', output='charmm.log', dump='result.pdb', debug=False, timeout=25.0)

Bases: object

A calculator to perform oragnic crystal structure optimization in CHARMM.

Parameters:

• struc – pyxtal.molecular_crystal.molecular_crystal object

• label (str) – label for this calculation

• algo (str) – “abnr”

• lat_mut (bool) – mutate lattice or not

• rotate (bool) – rotate lattice or not

• prefix (str) – prefix of this calculation

• atom_info (dict) – atom_labels

• folder (str) – folder name

• opt (str) – ‘conv’, ‘conp’, ‘single’

• steps (int) – optimization steps

• exe (str) – charmm executable

• input (str) – charmm input file

• output (str) – charmm output file

• dump (str) – charmm dump structure

FFTGrid(ABC)

determine the grid used for

clean()

execute()

read()

run(clean=True)

Only run calc if it makes sense

write(cutoff=14.0)

setup the necessary files for charmm calculation

class pyxtal.interface.charmm.PRM(input)

Bases: object

Parse, convert and merge PRM files for CHARMM

merge(prm1=None, single=None)

merge PRM into one

parse(prm)

parse prm list to get the dictionary

to_file(filename='test.prm')

Write the PRM file

to_string()

convert the PRM object to string

class pyxtal.interface.charmm.RTF(input)

Bases: object

Parse, convert, merge the RTF files for CHARMM

merge(rtf1=None, single=None)

merge two RTFs into one

parse(rtf)

parse rtf list to get the dictionary

parse_mass(mass)

to_file(filename='test.rtf')

Write the PRM file

to_string()

convert the RTF object to string

pyxtal.interface.charmm.check_prm(path)

Todo: move it to charmm interface Sometimes there are something wrong with prm file (RUBGIH),