[Openmm-betatesters] OpenMM 6.1 beta

[Peter Eastman]

The beta release of OpenMM 6.1 is now available and ready for testing!  This release contains lots of new features.

First, there are several new force fields.  These include:

- AMOEBA 2013.  This is a reparametrized version of the AMOEBA 2009 force field.  It uses the same functional form, but is more physically accurate.  It should be preferred over the old version for all purposes.

- The CHARMM polarizable force field.  This is a Drude based polarizable force field that attempts to get many of the same benefits as AMOEBA while being less expensive to calculate.

- TIP3P-FB and TIP4P-FB water models.  These are reparametrized versions of the TIP3P and TIP4P models that do a better job of matching experiment.

OpenMM also now has the ability to read CHARMM parameter and topology files.  This gives you yet another way to set up your systems for simulation.  It can now directly read files from nearly all the major simulation packages.

There are a couple of significant changes to improve performance.  First, AMOEBA now uses a different method to compute mutually induced dipoles (DIIS instead of SOR).  This typically requires only about half as many iterations, so it is much faster.  Second, the CPU platform now includes an optimized implementation of CustomNonbondedForce.  (In 6.0, it just used the reference implementation.)  This makes it many times faster than it was before, although it's still much slower than a standard NonbondedForce (unlike the CUDA and OpenCL platforms).

There is a new API for tabulated functions used in custom forces.  It now supports 2D and 3D functions, not just the 1D functions it had before.  Also, it now lets you distinguish between continuous and discrete functions.  In cases where a tabulated function is just being used as a lookup table, specifying that it's a discrete function can provide a big performance benefit.

There is a new type of virtual site called LocalCoordinatesSite.  This provides a very flexible calculation, and can support nearly any kind of virtual site that is computed based on three particles.

To download the beta, go to the regular downloads page (https://simtk.org/project/xml/downloads.xml?group_id=161) and click the "List all hidden releases" link just below the section for 6.0.1.  That link will only appear if you are logged in and are a member of the project.  If you aren't, send me your simtk.org username and I'll add you.

Thanks to all of you for helping to test this release!

Peter