OpenMD version 1.1.2

We are pleased to announce the release of OpenMD version 1.1.2. This version is largely a bugfix and performance release, and is recommended for all users of OpenMD. New things include:

  • Fixed a bug with FCFLAGS in the configure script
  • Fixed a configure script bug for qhull with C++ compilers
  • Fixed a bug with the conserved quantity in NPTxyz
  • Performance enhancements in main force loop (replaced slow anint with floor & ceiling) (10-20% speedup!)

OpenMD version 1.1.1

We are pleased to announce the release of OpenMD version 1.1.1. This version is largely a bugfix release, and is recommended for all users of OpenMD. New things include:

  • Fixed calls to getCharge for non-charge atoms (triggered by shifted pot / shifted force computations of self-self interactions without point charges on topologically connected molecules).
  • gcc 4.4 compatibility in ProgressBar
  • Revamped the visitor architecture to allow for easier conversion of internal data structures into xyz files for export and display.
  • Added svn revision numbering for banner display.

OpenMD version 1.1

We are pleased to announce the release of OpenMD version 1.1. This version fixes a number of bugs and provides extended functionality for some of the utility programs. It is recommended for all users of OpenMD. New things include:

  • Added a Progress bar to print out how long the simulation has remaining.
  • Fixed ConvexHull code and added “select hull” as valid selection syntax.
  • Fixed over-specificity in md-solvator and fixed installation bug.
  • Fixed parameter typo for minimizer.
  • Fixed gradients for minimization of rigid bodies
  • Added EAM line for Art Voter’s aluminium potential
  • Added NaN / INF detectors to DumpWriter and StatWriter
  • Added a new correlation function (gofrz) to do slab-segregated g(r) calculations. This computes at g(r) for pairs while requiring the z coordinates of the two sites to be at fixed separations. The data is output in: r, z, g(r,z).
  • Fixed a number of bugs in GhostBend and GhostTorsion.
  • Fixed a bug in Torsion (and GhostTorsion) triggered by configurations with colinear atoms. The problem was discovered by Brett Donovan. Thanks, Brett!
  • Added a new CosineBendType
  • Updated the visitor architecture to make it easier to extend
  • Updated Dump2XYZ to output velocities, forces, or vectors if requested.

OpenMD version 1.0.1

We are pleased to announce the release of OpenMD version 1.0.1 This version is largely a bugfix release, and is recommended for all users of OpenMD.  New things include:

  • Fixed the install procedures in the samples  and forceField directories.
  • Fixed Restraints, RestReader and RestWriter so that they work in parallel simulations.
  • Added a few new keywords to control how the constant-pressure hull method is invoked.
  • Added include lines for compatibility with gcc 4.4

OpenMD version 1.0

We are pleased to announce the release of OpenMD version 1.0. This version is a substantial rewrite and includes many new features relative to our old code (OOPSE):

  • A new MD (meta-data) input file format
  • Amber force field and numerous other changes to aid in protein simulation
  • New Hydrodynamics code to allow Langevin simulation of rigid bodies of arbitrary shapes (this is particularly useful for coarse-grained simulations)
  • New electrostatics code including the efficient damped-shifted-force method
  • A new Langevin Hull constant pressure algorithm