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Date: Fri, 3 Sep 2010 20:52:40 +0000
From: Aleksej Saushev <asau@netbsd.org>
Subject: CVS commit: pkgsrc/biology/gromacs
To: pkgsrc-changes@NetBSD.org
Reply-To: asau@netbsd.org
Message-Id: <20100903205240.1CF9F175DD@cvs.netbsd.org>
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Module Name:	pkgsrc
Committed By:	asau
Date:		Fri Sep  3 20:52:39 UTC 2010

Modified Files:
	pkgsrc/biology/gromacs: Makefile PLIST distinfo
	pkgsrc/biology/gromacs/patches: patch-aa patch-ag patch-ah
Removed Files:
	pkgsrc/biology/gromacs/patches: patch-ab patch-ac patch-af patch-ak

Log Message:
Update to GROMACS 4.5.1
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)


To generate a diff of this commit:
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/gromacs/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/gromacs/PLIST
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/gromacs/distinfo
cvs rdiff -u -r1.1.1.1 -r1.2 pkgsrc/biology/gromacs/patches/patch-aa
cvs rdiff -u -r1.1.1.1 -r0 pkgsrc/biology/gromacs/patches/patch-ab \
    pkgsrc/biology/gromacs/patches/patch-ac
cvs rdiff -u -r1.1 -r0 pkgsrc/biology/gromacs/patches/patch-af \
    pkgsrc/biology/gromacs/patches/patch-ak
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/gromacs/patches/patch-ag \
    pkgsrc/biology/gromacs/patches/patch-ah

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.