Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden). Existing SHA1
digests retained for now as an audit trail.
Do it for all packages that
* mention perl, or
* have a directory name starting with p5-*, or
* depend on a package starting with p5-
like last time, for 5.18, where this didn't lead to complaints.
Let me know if you have any this time.
a) refer 'perl' in their Makefile, or
b) have a directory name of p5-*, or
c) have any dependency on any p5-* package
Like last time, where this caused no complaints.
Notable changes in Gromacs 4.5.5:
* Improved pdb2gmx -chainsep option and reintroduced the -merge option.
* Fixed mdrun file appending truncating files to 0 bytes when
continuation runs stopped before writing new output.
* Fixed COM pulling with multiple constraints checking the
convergence of one constraint instead of all.
* Fixed some dihedrals in sugars in Gromos53a5/6 working on the wrong atoms.
* AmberGS force field is now based on Amber94 instead of Amber96.
* Moved hydrogens in Charmm27 protein termini to separate
charge groups and added ACE and CT3 residue types.
* Many small fixes which avoid termination with fatal errors
or crashes in mdrun and tools.
* Many small updates to the manual pages of programs.
* Fixed pdb2gmx picking up force field from local instead of
library directory
* Made pdb2gmx vsite generation work again for certain His namings.
* Fixed incorrect virial and pressure averages with certain
nst... values (instantaneous values correct)
* Fixed incorrect cosine viscosity output
* New -multidir alternative for mdrun -multi option
* Several minor fixes in analysis tools
* Several updates to the program documentation
This is maintainance release, it fixes:
* Double precision energy file reading
* CHARMM and GB issues
* Support for Altivec (PowerPC) with CMake
* Running binaries within the CMake build tree is now possible
* Various other issues
GROMACS 4.5.1 is bug fix release.
Release notes for 4.5
New features
* 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.
New tools
* g_bar: Bennett acceptance ratio (BAR) free energy calculations,
including automatic error estimates and phase space overlap
measures.
* g_rdf was a little bit enhanced that structure factors can
be calculated for any system, by supplying the necessary data
via sfactor.dat. Most of the common atomtypes are already
contained, but everybody who needs more freedom can enhance
the table
* g_select: Library support for "dynamic index groups" based
on textual selections (experimental feature).
See the tool g_select, the included template.c, or Doxygen
documentation for information on how to write analysis tools
using the library. Existing tools have not (yet) been
converted.
* g_tune_pme: For a given number of processes or threads this
tool systematically times mdrun with various numbers of
PME-only nodes and determines which setting is fastest. It
also checks whether performance can be enhanced by shifting
load between the real and the reciprocal space part of the
Ewald sum.
* g_membed: a very convenient utility for rapidly embedding
membrane proteins into equilibrated lipid bilayers
* g_pme_error: estimates the error of the electrostatic forces
if using the SPME algorithm. TO be incorporated in g_tune_pme
Changes that might affect your results
* grompp by default sets the new nstcalcenergy parameter equal
to nstlist, this has no effect on the integration, only on
the energy averages stored in ener.edr
* grompp by default sets the new nsttcouple parameter equal to
nstlist, this means T-coupling is done less frequently;
grompp checks if tau_t is large enough
* grompp by default sets the new nstpcouple parameter equal to
nstlist, this means P-coupling is done less frequently;
grompp checks if tau_p is large enough
* mdrun results with old tpr files with twin-range non-bonded
interactions will be different, because of the new symplectic
integrator
* for free-energy calculations sc-sigma now also sets the minimum
soft-core sigma (old tpr files retain the old behavior,
which can be enforced by setting the env.var. GMX_SCSIGMA_MIN to 0)
From pkgsrc-wip, packaged originally by Peter Ibsen Hansen.
GROMACS is a versatile package to perform molecular dynamics,
i.e. simulate the Newtonian equations of motion for systems with
hundreds to millions of particles.
