head 1.13; access; symbols pkgsrc-2023Q4:1.13.0.18 pkgsrc-2023Q4-base:1.13 pkgsrc-2023Q3:1.13.0.16 pkgsrc-2023Q3-base:1.13 pkgsrc-2023Q2:1.13.0.14 pkgsrc-2023Q2-base:1.13 pkgsrc-2023Q1:1.13.0.12 pkgsrc-2023Q1-base:1.13 pkgsrc-2022Q4:1.13.0.10 pkgsrc-2022Q4-base:1.13 pkgsrc-2022Q3:1.13.0.8 pkgsrc-2022Q3-base:1.13 pkgsrc-2022Q2:1.13.0.6 pkgsrc-2022Q2-base:1.13 pkgsrc-2022Q1:1.13.0.4 pkgsrc-2022Q1-base:1.13 pkgsrc-2021Q4:1.13.0.2 pkgsrc-2021Q4-base:1.13 pkgsrc-2021Q3:1.11.0.48 pkgsrc-2021Q3-base:1.11 pkgsrc-2021Q2:1.11.0.46 pkgsrc-2021Q2-base:1.11 pkgsrc-2021Q1:1.11.0.44 pkgsrc-2021Q1-base:1.11 pkgsrc-2020Q4:1.11.0.42 pkgsrc-2020Q4-base:1.11 pkgsrc-2020Q3:1.11.0.40 pkgsrc-2020Q3-base:1.11 pkgsrc-2020Q2:1.11.0.36 pkgsrc-2020Q2-base:1.11 pkgsrc-2020Q1:1.11.0.16 pkgsrc-2020Q1-base:1.11 pkgsrc-2019Q4:1.11.0.38 pkgsrc-2019Q4-base:1.11 pkgsrc-2019Q3:1.11.0.34 pkgsrc-2019Q3-base:1.11 pkgsrc-2019Q2:1.11.0.32 pkgsrc-2019Q2-base:1.11 pkgsrc-2019Q1:1.11.0.30 pkgsrc-2019Q1-base:1.11 pkgsrc-2018Q4:1.11.0.28 pkgsrc-2018Q4-base:1.11 pkgsrc-2018Q3:1.11.0.26 pkgsrc-2018Q3-base:1.11 pkgsrc-2018Q2:1.11.0.24 pkgsrc-2018Q2-base:1.11 pkgsrc-2018Q1:1.11.0.22 pkgsrc-2018Q1-base:1.11 pkgsrc-2017Q4:1.11.0.20 pkgsrc-2017Q4-base:1.11 pkgsrc-2017Q3:1.11.0.18 pkgsrc-2017Q3-base:1.11 pkgsrc-2017Q2:1.11.0.14 pkgsrc-2017Q2-base:1.11 pkgsrc-2017Q1:1.11.0.12 pkgsrc-2017Q1-base:1.11 pkgsrc-2016Q4:1.11.0.10 pkgsrc-2016Q4-base:1.11 pkgsrc-2016Q3:1.11.0.8 pkgsrc-2016Q3-base:1.11 pkgsrc-2016Q2:1.11.0.6 pkgsrc-2016Q2-base:1.11 pkgsrc-2016Q1:1.11.0.4 pkgsrc-2016Q1-base:1.11 pkgsrc-2015Q4:1.11.0.2 pkgsrc-2015Q4-base:1.11 pkgsrc-2015Q3:1.10.0.22 pkgsrc-2015Q3-base:1.10 pkgsrc-2015Q2:1.10.0.20 pkgsrc-2015Q2-base:1.10 pkgsrc-2015Q1:1.10.0.18 pkgsrc-2015Q1-base:1.10 pkgsrc-2014Q4:1.10.0.16 pkgsrc-2014Q4-base:1.10 pkgsrc-2014Q3:1.10.0.14 pkgsrc-2014Q3-base:1.10 pkgsrc-2014Q2:1.10.0.12 pkgsrc-2014Q2-base:1.10 pkgsrc-2014Q1:1.10.0.10 pkgsrc-2014Q1-base:1.10 pkgsrc-2013Q4:1.10.0.8 pkgsrc-2013Q4-base:1.10 pkgsrc-2013Q3:1.10.0.6 pkgsrc-2013Q3-base:1.10 pkgsrc-2013Q2:1.10.0.4 pkgsrc-2013Q2-base:1.10 pkgsrc-2013Q1:1.10.0.2 pkgsrc-2013Q1-base:1.10 pkgsrc-2012Q4:1.9.0.8 pkgsrc-2012Q4-base:1.9 pkgsrc-2012Q3:1.9.0.6 pkgsrc-2012Q3-base:1.9 pkgsrc-2012Q2:1.9.0.4 pkgsrc-2012Q2-base:1.9 pkgsrc-2012Q1:1.9.0.2 pkgsrc-2012Q1-base:1.9 pkgsrc-2011Q4:1.8.0.8 pkgsrc-2011Q4-base:1.8 pkgsrc-2011Q3:1.8.0.6 pkgsrc-2011Q3-base:1.8 pkgsrc-2011Q2:1.8.0.4 pkgsrc-2011Q2-base:1.8 pkgsrc-2011Q1:1.8.0.2 pkgsrc-2011Q1-base:1.8 pkgsrc-2010Q4:1.7.0.2 pkgsrc-2010Q4-base:1.7 pkgsrc-2010Q3:1.5.0.2 pkgsrc-2010Q3-base:1.5 pkgsrc-2010Q2:1.3.0.2 pkgsrc-2010Q2-base:1.3 pkgsrc-2010Q1:1.1.1.1.0.2 pkgsrc-2010Q1-base:1.1.1.1 pkgsrc-base:1.1.1.1 TNF:1.1.1; locks; strict; comment @# @; 1.13 date 2021.10.26.10.03.40; author nia; state Exp; branches; next 1.12; commitid R64ULQLy8JYkZieD; 1.12 date 2021.10.07.13.19.39; author nia; state Exp; branches; next 1.11; commitid CQ422EVgQgYxGSbD; 1.11 date 2015.11.02.18.42.21; author agc; state Exp; branches; next 1.10; commitid QWWynLrDLYuI4yHy; 1.10 date 2013.04.01.08.00.15; author sbd; state Exp; branches; next 1.9; 1.9 date 2012.01.14.00.38.18; author asau; state Exp; branches; next 1.8; 1.8 date 2011.03.23.05.36.29; author asau; state Exp; branches; next 1.7; 1.7 date 2010.11.23.19.43.58; author asau; state Exp; branches; next 1.6; 1.6 date 2010.10.21.12.03.57; author asau; state Exp; branches; next 1.5; 1.5 date 2010.09.03.20.52.39; author asau; state Exp; branches; next 1.4; 1.4 date 2010.07.31.19.14.08; author dholland; state Exp; branches; next 1.3; 1.3 date 2010.06.17.09.26.16; author asau; state Exp; branches; next 1.2; 1.2 date 2010.05.16.12.04.03; author asau; state Exp; branches; next 1.1; 1.1 date 2010.03.15.14.08.49; author asau; state Exp; branches 1.1.1.1; next ; 1.1.1.1 date 2010.03.15.14.08.49; author asau; state Exp; branches; next ; desc @@ 1.13 log @biology: Replace RMD160 checksums with BLAKE2s checksums All checksums have been double-checked against existing RMD160 and SHA512 hashes @ text @$NetBSD: distinfo,v 1.12 2021/10/07 13:19:39 nia Exp $ BLAKE2s (gromacs-4.5.5.tar.gz) = 5ea20182772ed1db559f752007db1716eb2a6bbeccbce1703d741be89d5c675e SHA512 (gromacs-4.5.5.tar.gz) = 8af0b81261a6b08c461275bccc4e72d23efd664ed5af12e3579956b5822ab6c6eea2ccbfbfe6ea1f4b30403a3c1367f52638e281cd1d7bc49e9220332c3e2b8c Size (gromacs-4.5.5.tar.gz) = 10398178 bytes SHA1 (patch-aa) = 60347ad02438d8e13c88c2267030b5793837a419 SHA1 (patch-ad) = 68b37154ba466e28cad0e539e25253c901421aaa SHA1 (patch-ae) = 59a5e88abeee883483b557cab1681c9a9098870f SHA1 (patch-ag) = 810d58d3ad787c9508f775674541775245402596 SHA1 (patch-ah) = 36ceeb409e59d8d3f0abe3bfa3ea3108f61f7a8e SHA1 (patch-ai) = ed4aa71eb56d1300c67cd17057f72ea452739f3d SHA1 (patch-aj) = 080d2923d729ff00de0f2cae75a82ec6c3769d6c @ 1.12 log @biology: Remove SHA1 hashes for distfiles @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.11 2015/11/02 18:42:21 agc Exp $ d3 1 a3 1 RMD160 (gromacs-4.5.5.tar.gz) = a3d40c3ac6ec9ee3e4607bd35afca1dd4715154e @ 1.11 log @Add SHA512 digests for distfiles for biology category. 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. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.10 2013/04/01 08:00:15 sbd Exp $ a2 1 SHA1 (gromacs-4.5.5.tar.gz) = ce4b4f9a0453dd2ffea72f28ea0bc7bb7a72f479 @ 1.10 log @Use host_alias for file paths (as it doesn't contain '-gnu'). @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.9 2012/01/14 00:38:18 asau Exp $ d5 1 @ 1.9 log @Update to Gromacs 4.5.5 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. @ text @d1 1 a1 1 $NetBSD$ d6 1 a6 1 SHA1 (patch-aa) = 29c6683c71989621f0f41682b1c225f524a2d84f @ 1.8 log @Update to Gromacs 4.5.4: * 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 @ text @d3 3 a5 3 SHA1 (gromacs-4.5.4.tar.gz) = c7b3fbd2f3ddf915bc082e7effe76a8276563726 RMD160 (gromacs-4.5.4.tar.gz) = 96065d1a173231f75869764a08eb4feccc1ec597 Size (gromacs-4.5.4.tar.gz) = 10353984 bytes @ 1.7 log @Update to Gromacs 4.5.3 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 @ text @d3 3 a5 3 SHA1 (gromacs-4.5.3.tar.gz) = c4845e5e62d1f53ee443301dad00138feba6d275 RMD160 (gromacs-4.5.3.tar.gz) = 2bb9cab3c611b93c4323e16b0d171c16cd407bf1 Size (gromacs-4.5.3.tar.gz) = 10338471 bytes @ 1.6 log @GROMACS team released another version a day after: 4.5.1-20100902-2d7e855 vs. 4.5.1-20100903-d982058 call it 4.5.1.1 This looks like bug fix, changes mostly affect NT, AIX, and HP-UX. @ text @d3 3 a5 3 SHA1 (gromacs-4.5.1.1/gromacs-4.5.1.tar.gz) = cbe52c3ec613fe8b652cd24b86c4fdf31b58c71b RMD160 (gromacs-4.5.1.1/gromacs-4.5.1.tar.gz) = 116ca5bc4644d1460086cfb2097961abd11db63b Size (gromacs-4.5.1.1/gromacs-4.5.1.tar.gz) = 10304547 bytes @ 1.5 log @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) @ text @d3 3 a5 3 SHA1 (gromacs-4.5.1.tar.gz) = 4352565278e39fb619208950780d8cb0b470a200 RMD160 (gromacs-4.5.1.tar.gz) = b28973526859359c84ba5d4fe2a5018b158f932b Size (gromacs-4.5.1.tar.gz) = 10300446 bytes @ 1.4 log @Fix destdir follies and resulting plist lossage. PR 43579. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.3 2010/06/17 09:26:16 asau Exp $ d3 4 a6 6 SHA1 (gromacs-4.0.7.tar.gz) = 8519bef2fa989fb487d54612b0a2d0228f228b30 RMD160 (gromacs-4.0.7.tar.gz) = 4fa8e5c90f549ef627a98a907a166676692a4c4b Size (gromacs-4.0.7.tar.gz) = 8404518 bytes SHA1 (patch-aa) = dcf39e862c2087bca0cd4e577438633bf70fe57f SHA1 (patch-ab) = 333fea1f0844f8628795f593de16c941744b11d2 SHA1 (patch-ac) = 164a7b3e06ab4f4cc1142615c1281eec82adee9b d9 2 a10 3 SHA1 (patch-af) = 58e97df84e64e071257fd36d09840ef719461ea5 SHA1 (patch-ag) = 5d46a0dba7db4dbf08ea83d448a6e5201871d217 SHA1 (patch-ah) = ad930cbb9f448780ca8745b899fe54c5470fff3b a12 1 SHA1 (patch-ak) = bdfebf85422a6a9025d1f2c71921c4cc1c3069c4 @ 1.3 log @Add tag to libtool invocations, where necessary. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.2 2010/05/16 12:04:03 asau Exp $ d16 1 @ 1.2 log @Build with MPI support by default. Introduce "mpi" option to turn the above off. Bump PKGREVISION. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.1.1.1 2010/03/15 14:08:49 asau Exp $ d10 6 @ 1.1 log @Initial revision @ text @d1 1 a1 1 $NetBSD$ d9 1 @ 1.1.1.1 log @Import GROMACS 4.0.7 as biology/gromacs. 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. @ text @@