Package schrodinger :: Package application :: Package desmond :: Module remd
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Module remd

Utilities for REMD.

Copyright Schrodinger, LLC. All rights reserved.

Functions [hide private]
 
is_water(site, constraint)
 
get_nonduplicated_atom(ct)
 
get_num_wateratom(model, selected_atom)
 
get_num_nonwateratom(model, selected_atom)
 
get_num_constraint(model, selected_atom)
 
get_degrees_of_freedom(model, selected_atom)
 
predict_temperature_ladder(temp, exchange_probability, model, asl, should_fix=True)
`temp' should be a two-tuple, specifying the temperature range.
 
predict_with_temp_and_exch(temp, exchange_probability, model, asl)
Given temperature range and exchange_probability, predicts the number of replica and returns the temperature ladder.
 
predict_with_nreplica_and_exch(n_replica, exchange_probability, base_temp, model, asl)
Given the base temperature, number of replicas, and exchange_probability, predicts the top temperature and returns the temperature ladder.
 
predict_with_temp_and_nreplica(temp, n_replica, model, asl)
Given the temperature range and number of replicas, predicts the exchange probability and returns the temperature ladder.
 
split_ct(ct, selected_atom)
 
set_freezing_atommass(model, mass_scale)
 
freeze_atom(model, asl, frozen_atom_mass_threshold=1000000000.0)
 
rescale_ff(ct, atom_list, scaling_factor)
 
rescale_ff_solute_tempering(model, out_fname, asl, scaling_factor)
 
test_get_num_wateratom(model)
 
test_get_num_nonwateratom(model)
 
test_get_num_constraint(model)
 
test_get_degrees_of_freedom(model)
 
test_predict_temperature(model)
 
test_freeze_atom(model)
 
test_predict_with_nreplica_and_exch(model)
 
test_predict_with_temp_and_nreplica(model)
Variables [hide private]
  erf = <ufunc 'erf'>
  FROZEN_ATOM_MASS_THRESHOLD = 1000000000.0
  model = cms.Cms(file= "test.cms")
  __package__ = 'schrodinger.application.desmond'
Function Details [hide private]

predict_temperature_ladder(temp, exchange_probability, model, asl, should_fix=True)

 

`temp' should be a two-tuple, specifying the temperature range. `model' should be a `Cms' object.