schrodinger.application.desmond.gconfig

Module gconfig

Utilities for handling gDesmond config files.

Functions

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get_default_setting(msj)

get_exec_name(msj)

get_exec(msj, cfg)

is_minimize(msj)

is_meta(msj)

is_vrun(msj)

is_remd(msj)

has_plugin(desmond_exec, plugin_name)

add_plugin(desmond_exec, plugin_name, position=None)

remove_plugin(desmond_exec, plugin_name)

get_homebox(box, cpu_top)

is_triclinic_box(box)

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 = "...

msj = sea.Map(open(sys.argv [1], "r").read())

model = cms.Cms(file= sys.argv [2])

cfg = msj2cfg(msj, None, model, {"$JOBNAME": "test",})

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
...