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).].

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).

  • model – should be a Cms object.


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>.