[MMTK] MMTK 2.1.2

[Konrad Hinsen]

It has been a while since the last MMTK release, and although there
are no ground-breaking new features, the bug fixes and performance
optimizations might well be interesting for some users, so I decided
to publish a new development release, MMTK 2.1.2, available immediately
at

    ftp://dirac.cnrs-orleans.fr/pub/MMTK/

There is also a new release of ScientificPython, version 2.1.3, available
from

    ftp://dirac.cnrs-orleans.fr/pub/ScientificPython/

MMTK 2.1.2 does not require an update of ScientificPython, except for
profiting from the new features in the TrajectoryViewer tool.

The following excerpt from the change log summarizes the evolution
since the last stable release, MMTK 2.0:

---------------------------------------------------------------------------

2.1.1 --> 2.1.2
===============

New features:

- The TrajectoryViewer tool (in Tools/TrajectoryViewer) was extended
  by normal mode projections for proteins.

- The structure of trajectory files can be influenced by specifying
  a "block size", which can be used to optimize I/O performance on
  very large files.

- Reading of single-atom and rigid-body trajectories has been
  optimized.


Bug fixes:

- The functions MMTK.Biopolymers.defineAminoAcidResidue and
  MMTK.Biopolymers.defineNucleicAcidResidue didn't work.

- The method MMTK.Collection.GroupOfAtoms.findTransformationAsQuaternion
  returned randomly one of the two equivalent quaternions that desribe
  the rigid-body rotation. This doesn't matter for most purposes, but
  it creates non-continuous quaternion trajectories when applied to a
  sequence of configurations. The method has been changed to return
  the quaternion that has a positive real part.

- Rigid-body trajectories (in module Trajectory) were wrong in certain
  circumstances.


2.1.0 --> 2.1.1
===============

Modifications:

- Improved load balance for shared memory parallelization.

- The united-atom models for amino acids were changed from Amber 91
  conventions to OPLS by removing the fake "lone pair" atoms.
  Note that there was never proper support for lone pair atoms, so
  this model wasn't functional, and therefore nothing should be
  broken by this change. Now the united-atom model is actually
  fully usable together with the OPLS force field.
  (Thanks to Krzysztof Murzyn for fixing this!)

Additions:

- Basic MPI support. Only energy evaluation has been parallelized,
  using a data-replication approach. All processors execute the same
  code and cooperate only during energy evaluation. See
  the Example MPI/md.py for more information.

- New force fields: HarmonicForceField, CalphaForceField, SPCEForceField.
  The first two are designed for proteins, the last one is only for
  water.


2.0 --> 2.1.0
=============

Bug fixes:

- Addition of force fields didn't work when one of the terms was
  already a compound force field.

- Memory allocation bug in DCD output.

- Restarting NPT dynamics simulations didn't work due to a reported
  universe mismatch. This was caused by the different box size.

- MMTK.DCD.writeDCDPDB produced a PDB file with non-contiguous molecules for
  periodic universes.

- In the electrostatic options for the Amber force field, the "screened"
  option was misinterpreted as "ewald".

Modifications:

- The method objectList() for collections and universes now takes
  an optional argument specifying a class; only the objects corresponding
  to this class are returned. This permits a simple identification of
  proteins etc.

- The universe description that is stored in a trajectory now contains
  the force field and environment objects (thermostats and barostats).

- Optional name argument for C evaluator objects for bonded
  interactions.

Additions:

- Thread support.

- Module MMTK.ForceFields.Restraints.

- New function MMTK.DCD.writeVelocityDCDPDB for exporting velocities
  to velocity DCD files.

- New method pairIndices for nonbonded list objects.

---------------------------------------------------------------------------

As always, I am interested in all the feedback you can provide.

Konrad.
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                            | E-Mail: hinsen@cnrs-orleans.fr
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69
Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
France                                   | Nederlands/Francais
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