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Release Name: Zephyr 2.0

Change Log

Version 2.0.2 July 8, 2010
* Latest (release?) version of OpenMM 2.0 libraries
* Position restraint step removed because it often fails

Version 2.0.0 June 23, 2010
* Cancel button works better on Mac and Linux
* Based on OpenMM 2.0
* OpenCL support on all platforms
* Many changes related to supporting explicit solvent simulations.
* genion executable added
* mdrun_openmm now supports thermostat, barostat, position restraint.
* Added amber ff99sb and ff03 force fields

Version 1.1.2 Feb 12, 2010
* Avoid uninitialized mdrunWorkingDirectory problem on machines 
running Zephyr for the first time.

Version 1.1.1 Feb 12, 2010
* Use mac binaries from snow build machine, to match OpenMM 1.1 files

Version 1.1.0 beta: Feb 11, 2010
* Uses nightly build binaries from Feb 11 (might be OpenMM 1.1 
* Added tooltips to help with new continuation functionality

Version 1.0 beta2
* Continuation uses trajectory (trr) files
* No longer supports PPC Mac, nor Mac OS 10.4 (Tiger)
* OpenMM no longer supports ATI GPUs

Version 1.0 beta
* Uses OpenMM 1.0 beta release.
* Initial coordinates now written to first frame of trajectory file.
* Continuation of previous run from molecules panel added.

Version 0.9.4: Sep 30, 2009
* Advanced parameters dialog containing all OpenMM-relevant mdp file
* Checkpoint files are created at the end of each run.
* Option to restart using a checkpoint file.
* Permit choosing a non-existent simulations directory
* Fixed bug where simulation would fail if default simulations
directory does not exist.
* "Cancel" button creates checkpoint file on Linux (but not on 
* A new simulation subdirectory is created for each new input pdb 
* Zephyr remembers where VMD and your top-level simulation directory 

Version 0.9.2: Sep 25, 2009
* Changes to dialogs and "About" panel.

Version 0.9.1: 
* Changed WIndows VS8 redistributable installer to a better one.
* Don't remove HETATMs from pdb files, but do remove waters.

Version 0.9.0: Aug 31, 2009
* New binaries based on OpenMM Preview Release 4 
* Automatic conversion of PDB files to ffamber format 
* First 64-bit Linux support

Version 0.8.3: June 8, 2009
* User manual updated
* PDB files in testData directory rearranged

Version 0.8.2: May 21, 2009
* Patch to use correct GBSA scale factors for phosphorus atoms
* Experimental Linux installer created

Version 0.8.1: May 18, 2009
* Using binaries built using OpenMM Preview Release 3

Version 0.7.4: May 11, 2009
* Heartbeat-per-second timing messages no longer sent to log file nor 
* "faster folding" option reworded to "faster dynamics"
* g_energy and tpbconv executables added to bin directory
* Possible fix for rare dialog 'Error: could not read "md.log": no 
such file or directory'  (Though the dialog did not appear to 
interfere with the simulation.)
* "doc" directory no longer installed inside of Mac app bundle

Version 0.7.3:
* Even more villin structure files added to testData directory
* Final structure file at end of dynamics run is now in .gro format,
instead of broken .pdb format (issue 798)
* Reporting of elapsed an remaining time is more consistent (issue 
* Frequency of writing trajectory frames automatically changes to
equal the minimum of VMD output frequency and total run time (issue 

Version 0.7.2: 
* nvidia GPU accelerated platform works on Mac (issue 787)

Version 0.7.0: Apr 20, 2009
* Selecting VMD application bundle on Mac now works
* zephyr.log file is created for later perusal
* resizing Zephyr window keeps more critical information at smaller 
* Mac Zephyr runs on intel and powerpc CPUs
* Mac Zephyr works when client does not have X11 installed
* Mac Zephyr works with OS X 10.4
* Gromacs and VMD input commands are now blue instead of red (less 
* Degree symbol repaired on parameters panel
* Version number moved to "About" panel
* No Tcl/Tk installation is required
* Default simulations directory is in the user's home directory

Version 0.6.7/8: Apr 16, 2009

Version 0.6.4: Apr 7, 2009
* Does not require previous Tcl/Tk installation on client computer. 
* First release with Mac OS X version.

Version 0.5.0: Feb 9, 2009
* ATI simulation works with alanylalanine 
* Collision interval variable exposed 
* GPU paper reference added to "About" dialog

Version 0.4.2: Feb 4, 2009

Version 0.3.1: Jan 30, 2009
* Uses NSIS installer. 
* Molecules page modified after user testing. 
* Cancel button actually kills Windows processes now.

Version 0.2: Jan 29, 2009

Version 0.1: Jan 16, 2009