[gmx-announce] New release: 4.5.3

[Rossen Apostolov]

Dear Gromacs users and developers,

It's been quite some time since the last posting to this list - Oct 2005 
when 3.3 was out.

We have released 4.5 a few months ago with a lot of new functionality:


     * Pencil decomposition of the reciprocal space PME grid to improve 
scaling. This reduces the amount of communication for high 
parallelization and improves load balancing with up to 40% overall 
performance improvement for large systems.
     * Memory usage is improved for very large systems, allowing 
simulations of >100 million atoms.
     * Running on a multi-core node now uses thread-based 
parallelization to automatically spawn the optimum number of threads in 
the default build. MPI is now only required for parallelization over the 
network.
     * Domain decomposition can now also be used without periodic 
boundary conditions
     * GPU acceleration support on NVIDIA cards. This first release with 
GPU support based on OpenMM provides up to an order of magnitude faster 
performance for implicit solvent simulations, but PME simulations are 
about as fast as on a high-end CPU.
     * Check-pointing is made more secure:MD5sum are used to verify that 
all files are correctly in-place before a simulation is appended. Output 
file appending at continuation is turned on by default.
     * Increased tolerance for networked file system failures and 
cluster node crashes: checkpoint handling is safer and mdrun forces file 
system cache flushes during checkpoints.
     * Full CMake support. After the 4.5 release we will be switching 
the default build tool from autoconf to cmake, and possibly deprecate 
autoconf in the future.
     * Full support for seven AMBER force fields in the standard 
distribution, with default Amber names. We also include the recent 
Amber99sb-ildn in the distribution.
     * Support for CHARMM27, including cmap for dihedrals
     * Efficient Generalized-Born implicit solvent support including the 
Still/HCT/OBC-models to compute the Born radii, a novel way of 
tabulating the generalized Born-interaction formula for greater speed, 
and optimized SSE-routines in both single and double precision.
     * Highly efficient all-vs-all assembly kernels for both vanilla and 
generalized born interactions, in both single and double precision.
     * Much better support for nucleic acid simulations, including 
automatic handling by pdb2gmx.
     * Support for Velocity-Verlet integrators for reversible T- and 
P-coupling; MTTK pressure control integrators; Nose-Hoover chains.
     * Symplectic Trotter Leap-Frog integrator for twin-range non-bonded 
interactions.
     * Support for Bennet acceptance ratio calculations through direct 
calculation of Hamiltonian differences during the simulation.
     * File formats: All GROMACS tools can now read any VMD supported 
trajectory format, without converting trajectory first. (VMD libraries 
are required).
     * pdb2gmx now retains the residue numbers from the input, mdrun and 
all tools use these original numbers.


A new maintenance release of Gromacs 4.5 is now available: 
ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.3.tar.gz.

Thanks again to all for the contributions!

Happy simulating!
Rossen