Project Filelist for Molecular Modelling Toolkit
File Release Notes and Changelog
Release Name: 2.7.2
Improvements: - ParticleProperty objects (including ParticleScalar, ParticleVector, and Configuration objects) have a new method selectAtoms. Its argument is a function that is called with the property of one particle and returns a boolean deciding whether or not that particle is part of the selection. - CalphaForceField has a new option (version=2) for the pair force constants. For reasonable input structures, it is equivalent to the default, version=1. It adds a threshold for small nearest-neighbour C-alpha distances: for distances less than 0.37 nm, the force constant does not decrease below its value at 0.37 nm. This ensures that the Hessian remains positive semi-definite for proteins with unrealistically short C-alpha distances. - MMTK.Subspae.Subspace has a new method complement() which returns the orthogonal complement. - Two new example scripts: - Miscellaneous/bad_contacts.py - Miscellaneous/two_models.py - Protein friction constants for Brownian Dynamics (module MMTK.ProteinFriction) are calculated with a threshold that assures a minimal value of 1000/ps. Without this threshold, friction constants could become negative for solvent-exposed loops. Bug fixes: - The VelocityVerletIntegrator could crash, or produce NaN results, for systems with distance constraints and a thermostat but no barostat. - All examples now work with recent releases of NumPy. - Installation could break on systems whose C compiler's sizeof returns another type than "int". - Trajectory actions of type "function" could crash integrators.
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