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.

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

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