schrodinger.application.desmond.predict_remd_temp module

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.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.desmond.predict_remd_temp.predict_temperature(low_temp, high_temp, exchange_probability, model, frozen_atom_mass_threshold=1000000000.0, should_fix=True)

Parameters

• low_temp – minimum temperature

• high_temp – maximum temperature

• exchange_probability – A good default is 30% (0.3).

• model – should be a Cms object.

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.

schrodinger.application.desmond.predict_remd_temp.freeze_atoms(model, asl, frozen_atom_mass_threshold=1000000000.0)

Freeze atoms in <model> specificed by the <asl>.