[gmx-announce] New release: 4.5.3
Rossen Apostolov
rossen at kth.se
Wed Nov 10 21:17:54 CET 2010
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
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