Package schrodinger :: Package application :: Package desmond :: Module gconfig
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Module gconfig

Utilities for handling gDesmond config files.

Copyright Schrodinger, LLC. All rights reserved.

Functions [hide private]
 
real_to_int(val)
round up to the closest integer when the difference is less than 1e-7
 
optimize_key(msj, cfg, model)
Optimizes the simulation parameters in 'cfg', where 'cfg' must represent a complete config file.
 
parse_lambda(s)
 
lambda_type(lambda_)
 
num_lambda_window(lambda_)
 
__calc_vdw_lambda(n_win)
Given the number of windows, returns a list of lambda values for VDW potentials.
 
__calc_charge_lambda(n_win)
 
__calc_bonded_lambda(n_win)
 
__get_fep_schedule(n_win, fep_type='alchemical', scheme='default')
Returns a FEP schedule, which is calculated for the given FEP type ('fep_type').
 
__set_fep(msj, cfg, model)
 
__set_meta(msj, cfg, model)
 
__set_cutoff_radius(msj, cfg, model)
 
__set_bigger_rclone(msj, cfg, model)
 
__set_taper(msj, cfg, model)
 
__set_coulomb_method(msj, cfg, model)
 
__set_temperature(msj, cfg, model)
 
__set_annealing(msj, cfg, model)
 
__set_pressure(msj, cfg, model)
 
__set_surface_tension(msj, cfg, model)
 
get_ensemble_class_method(msj)
 
__set_ensemble(msj, cfg, model)
 
__set_time(msj, cfg, model)
 
__set_elapsed_time(msj, cfg, model)
 
__set_timestep(msj, cfg, model)
 
__set_cpu(msj, cfg, model)
 
__set_glue(msj, cfg, model)
 
__set_vrun_frameset(msj, cfg, model)
 
__set_trajectory(msj, cfg, model)
 
__set_eneseq(msj, cfg, model)
 
__set_checkpt(msj, cfg, model)
 
__set_maeff_output(msj, cfg, model)
 
__set_randomize_velocity(msj, cfg, model)
 
__set_simbox(msj, cfg, model)
 
get_simbox_output_filename(msj)
Returns 'None' if the simbox_output plugin is turned off.
 
__set_energy_group(msj, cfg, model)
 
get_energy_group_output_filename(msj)
Returns 'None' if the energy_groups plugin is turned off.
 
get_fep_output_filename(msj)
 
__set_max_steps(msj, cfg, model)
 
__set_convergence(msj, cfg, model)
 
__set_steepest_descent_steps(msj, cfg, model)
 
__set_num_vector(msj, cfg, model)
 
__set_backend(msj, cfg, model)
 
gen_temperature_for_solute_tempering(setting, model, base_temp, asl, printer=None)
 
gen_replica(msj, model=None)
 
__set_replica(msj, cfg, model)
 
get_replica_setting(msj)
 
__set_model_file(msj, cfg, model)
 
__attach_msj(msj, cfg, model)
 
__optimize_cfg(msj, cfg, model)
 
__clean_cfg(cfg)
 
__fix_cfg(msj, cfg)
 
__msj2cfg_helper(msj, cfg, model, macro)
 
msj2cfg(msj, cfg, model, macro={})
Variables [hide private]
  DEFAULT_CONFIG = '{\napp = mdsim # mdsim | remd |\nbo...
  msj = sea.Map(open(sys.argv [1], "r").read())
  model = cms.Cms(file= sys.argv [2])
  cfg = msj2cfg(msj, None, model, {"$JOBNAME": "test",})
  __package__ = 'schrodinger.application.desmond'
Function Details [hide private]

__get_fep_schedule(n_win, fep_type='alchemical', scheme='default')

 

Returns a FEP schedule, which is calculated for the given FEP type ('fep_type').

Parameters:
  • fep_type - Can take the following values: "alchemical", "binding".

Variables Details [hide private]

DEFAULT_CONFIG

Value:
'''{
app       = mdsim    # mdsim | remd |
boot.file = filename

global_cell = {
   reference_time       = 0.0
   topology             = periodic
   n_replica            = 1
...