Enhanced sampling

Enhanced sampling#

openmicron.forcefield.functionterms.umbrella_sampling_contact(cv_info, kums, q0, beta=50, lamda=1.2, force_group=12)[source]#

Implementing umbrella sampling for contacts

Parameters:

  • cv_info (pd.DataFrame) – The information for the contacts is expressed in a table format of N rows, where N represents the number of contacts. Each row consists of three columns: index (a1, a2), and the corresponding rest length (sigma) for each contact.

  • kums (float) – The spring constant

  • q0 (float) – The center of each harmonic biasing potential. The values of q0 cover the range from 0 to 1.

  • beta (float) – The smoothing parameter that default value is 50 and unit is nm.

  • lamda (float) – The scale parameter of rest length. default value is 1.2.

  • force_group (int) – Force group.

Returns:

ums_contact

Return type:

openmm force

Contents