Changes, bug fixes, and older versions

The latest version of brownmove with all the fixes described below can be downloaded here (get brownmove_1.4.tgz) Updated versions of the code are referenced at the respective descriptions.

Version 1.3 was an internal release.

Changes since the last version V1.2 (get brownmove_1.2.tgz):

  • Sep 25, 2012: some more includes of stdlib.h and stdio.h for gcc 4.6, updated Perl files of the tutorials to work under Ubuntu 12.04 LTS
  • added setup files for nanobead agglomeration publication [Geyer, Born, Kraus, PRL 109 (2012) 128302]
  • new vdWShape interactions (nanobead potential, linear)
  • new sticky interactions (transient bonds)
  • parser upgrade: include files, evaluations, counters

Changes since the last version V1.1 (get brownmove_1.1.tgz):

  • added setup files for BMC Biophysics (2011) manuscript on “Many-particle Brownian and Langevin Dynamics Simulations with the Brownmove package”
  • Feb 22, 2011: Parsers not don’t care about case anymore — only names of shapes and constants remain case sensitive
  • Feb 9, 2011: Corrected EstatShape: torques point into the correct direction again (introduced as a side effect of some code cleanup :-(
  • Jan 20, 2011: brownmove now accepts definition of constants on the commandline (-d <variable name> “<value>”)
  • Nov 9, 2010: main loop catches Ctrl-C (and various other signals) and exits gracefully
  • Nov 8, 2010: included <stdlib.h> in vdwshape.h for GCC >= 4.3 (else exit() is not defined)

Changes since the original release of V1.0 (get brownmove_1.0.tgz with all updates included):

  • Nov.23, 2009: some debug code in hishape.cpp was not commented out, leading to a lot of logging to stderr. New version of hishape.cpp.
  • Nov. 6, 2009: bug in vdWShape: in the interaction between spheres and blocks, the vdW color of the spheres was not queried, leading to a segmentation fault due to random memory access. New version of vdwshape.cpp.
  • Nov. 4, 2009: the reflective walls in wall.cpp were changed. Now the protein’s CM is reflected back into the simulation instead the individual gestalt objects. Now the CM has a chance to get behind the wall and trigger an acceptor. (Did not affect proteins with a single shape). New version of wall.cpp.
  • Compilation with GCC 4.3 fails: compiler complains about undefined functions — some stuff is not included by default any more. Fix: #include <stdlib.h> and <string.h> in externalshape.h, proteinparser.h, and brownmove.cpp (is fixed in the archive).

The first release: 1.0RC1 (get brownmove_1.0RC1.tgz)