schrodinger.application.desmond.predict_remd

Module predict_remd_temp

A script for predicting temperature profile for REMD simulations. The prediction is based on the work by Patriksson and van der Spoel [Phys. Chem. Chem. Phys., 10:2073-2077 (2008). http://dx.doi.org/10.1039/b716554d].

This script can optionally generate a new .cms file with a portion of the system made frozen. Such a treatment can increase the temperature span of REMD.

Functions

[hide private]

erf(x)

_is_water(site_block, constraint)

_get_num_wateratom(model, frozen_atom_mass_threshold=FROZEN_ATOM_MASS_THRESHOLD)

_get_num_nonwateratom(model, frozen_atom_mass_threshold=FROZEN_ATOM_MASS_THRESHOLD)

_get_num_constraint(model, frozen_atom_mass_threshold=FROZEN_ATOM_MASS_THRESHOLD)

_get_degrees_of_freedom(model, frozen_atom_mass_threshold=FROZEN_ATOM_MASS_THRESHOLD)

predict_temperature(low_temp, high_temp, exchange_probability, model, frozen_atom_mass_threshold=FROZEN_ATOM_MASS_THRESHOLD, should_fix=True)
low_temp - minimum temperature high_temp - maximum temperature exchange_probability - A good default is 30% (0.3).

_split_ct(ct, selected_atom)

_set_freezing_atommass(model, mass_scale)

freeze_atoms(model, asl, frozen_atom_mass_threshold=FROZEN_ATOM_MASS_THRESHOLD)
Freeze atoms in <model> specificed by the <asl>.

Variables

[hide private]

FROZEN_ATOM_MASS_THRESHOLD = 1E9

cmd = cmdline.SingleDashOptionParser(usage= "$SCHRODINGER/run ...

num_args = len(args)

in_fname = args [0]

temp = opt.temp.split()

num_temp = len(temp)

low_temp = float(temp [0])

high_temp = float(temp [1])

model = cms.Cms(file= opt.out)

sys_fname = opt.out

i = 1

Function Details

[hide private]

predict_temperature(low_temp, high_temp, exchange_probability, model, frozen_atom_mass_threshold=FROZEN_ATOM_MASS_THRESHOLD, should_fix=True)


low_temp - minimum temperature
high_temp - maximum temperature
exchange_probability - A good default is 30% (0.3). FIXME add a description
model - should be a `Cms' object.
frozen_atom_mass_threshold - FIXME add a description
should_fix - FIXME add a description

Returns a tuple of (temp_profile, prob_profile).
    temp_profile is a list of temperature values.
    prob_profile is a list of predicted exchange probabilities.

Variables Details

[hide private]

cmd

Value:

cmdline.SingleDashOptionParser(usage= "$SCHRODINGER/run %prog [options
] <input .cms file>\n\n" "A script for predicting temperature profile 
for REMD simulations.\n" "It can optionally generate a new .cms file w
ith a designated\n" "portion of the system made effectively frozen. Su
ch a treatment can\n" "increase the temperature span of REMD.", versio
n_source= "$Revision: 1.7 $")