[Openmm-betatesters] OpenMM 6.3 beta

[Peter Eastman]

A beta of OpenMM 6.3 is now available for download.  There are lots of improvements and new features in this release.  Here are some of the more significant ones.

The biggest and most important new feature is support for triclinic periodic boxes.  This involves very few API changes.  The System class already allowed you to specify arbitrary box vectors, but previously threw an exception if they weren't aligned with the axes.  It now accepts other box shapes.  Likewise, loading files (PDB, etc.) that define triclinic boxes now works exactly as you would expect.

We've done a lot of optimization work in this release, especially to the CPU and OpenCL platforms.  Simulations using PME with those platforms should now be about 15% faster than before.  Memory use is also reduced in certain situations.

A number of new methods have been added to the Simulation class to simplify common operations, such as running a simulation for a fixed amount of clock time, and writing checkpoints during a simulation.

The rRESPA and aMD integrators have now been made into core features.  They were previously available from the add-on repository (http://wiki.simtk.org/openmm/VirtualRepository), but now they're included in the main installer.

It can now take advantage of the runtime compilation API added in CUDA 7.0.  This means that when you're using CUDA 7.0, an external compiler is no longer required and you no longer need to set environment variables to tell it how to find nvcc.

The OpenCL platform has returned to OS X!  As of Mac OS X 10.10.3, Apple has finally fixed the last of their critical OpenCL bugs, so we are able to make that platform available again (but only enabled on 10.10.3 or later).

There is a new barostat specifically for RPMD simulations.  The standard barostats didn't work correctly with RPMDIntegrator, so we have created a new one that allows pressure regulation to be done correctly with RPMD.

When using Modeller.addSolvent() to build a water box around a system, there is a new option to add a fixed number of water molecules, rather than building a box of fixed size with an unspecified number of molecules.

Several new functions are now available in custom expressions, including floor(), ceil(), and select().

One important change to be aware of: the precompiled binaries for Windows are now 64 bit, not 32 bit.  This was required by the move to CUDA 7.0, since they no longer provide 32 bit versions of some libraries.  This means you need to use 64 bit versions of Python and FFTW as well.  Also note that the manual has not yet been updated to reflect this change: it still says to use 32 bit versions.  That will be corrected in the final release.

OpenMM 6.3 beta is available from https://simtk.org/project/xml/downloads.xml?group_id=161.  Scroll to the bottom of the section for 6.2 and click the link that says, "List all hidden releases."  That link will only appear if you're logged in to simtk.org and you're a member of the project, so if you aren't, email me your user name and I'll add you.

Peter