head 1.7; access; symbols pkgsrc-2023Q4:1.7.0.96 pkgsrc-2023Q4-base:1.7 pkgsrc-2023Q3:1.7.0.94 pkgsrc-2023Q3-base:1.7 pkgsrc-2023Q2:1.7.0.92 pkgsrc-2023Q2-base:1.7 pkgsrc-2023Q1:1.7.0.90 pkgsrc-2023Q1-base:1.7 pkgsrc-2022Q4:1.7.0.88 pkgsrc-2022Q4-base:1.7 pkgsrc-2022Q3:1.7.0.86 pkgsrc-2022Q3-base:1.7 pkgsrc-2022Q2:1.7.0.84 pkgsrc-2022Q2-base:1.7 pkgsrc-2022Q1:1.7.0.82 pkgsrc-2022Q1-base:1.7 pkgsrc-2021Q4:1.7.0.80 pkgsrc-2021Q4-base:1.7 pkgsrc-2021Q3:1.7.0.78 pkgsrc-2021Q3-base:1.7 pkgsrc-2021Q2:1.7.0.76 pkgsrc-2021Q2-base:1.7 pkgsrc-2021Q1:1.7.0.74 pkgsrc-2021Q1-base:1.7 pkgsrc-2020Q4:1.7.0.72 pkgsrc-2020Q4-base:1.7 pkgsrc-2020Q3:1.7.0.70 pkgsrc-2020Q3-base:1.7 pkgsrc-2020Q2:1.7.0.66 pkgsrc-2020Q2-base:1.7 pkgsrc-2020Q1:1.7.0.46 pkgsrc-2020Q1-base:1.7 pkgsrc-2019Q4:1.7.0.68 pkgsrc-2019Q4-base:1.7 pkgsrc-2019Q3:1.7.0.64 pkgsrc-2019Q3-base:1.7 pkgsrc-2019Q2:1.7.0.62 pkgsrc-2019Q2-base:1.7 pkgsrc-2019Q1:1.7.0.60 pkgsrc-2019Q1-base:1.7 pkgsrc-2018Q4:1.7.0.58 pkgsrc-2018Q4-base:1.7 pkgsrc-2018Q3:1.7.0.56 pkgsrc-2018Q3-base:1.7 pkgsrc-2018Q2:1.7.0.54 pkgsrc-2018Q2-base:1.7 pkgsrc-2018Q1:1.7.0.52 pkgsrc-2018Q1-base:1.7 pkgsrc-2017Q4:1.7.0.50 pkgsrc-2017Q4-base:1.7 pkgsrc-2017Q3:1.7.0.48 pkgsrc-2017Q3-base:1.7 pkgsrc-2017Q2:1.7.0.44 pkgsrc-2017Q2-base:1.7 pkgsrc-2017Q1:1.7.0.42 pkgsrc-2017Q1-base:1.7 pkgsrc-2016Q4:1.7.0.40 pkgsrc-2016Q4-base:1.7 pkgsrc-2016Q3:1.7.0.38 pkgsrc-2016Q3-base:1.7 pkgsrc-2016Q2:1.7.0.36 pkgsrc-2016Q2-base:1.7 pkgsrc-2016Q1:1.7.0.34 pkgsrc-2016Q1-base:1.7 pkgsrc-2015Q4:1.7.0.32 pkgsrc-2015Q4-base:1.7 pkgsrc-2015Q3:1.7.0.30 pkgsrc-2015Q3-base:1.7 pkgsrc-2015Q2:1.7.0.28 pkgsrc-2015Q2-base:1.7 pkgsrc-2015Q1:1.7.0.26 pkgsrc-2015Q1-base:1.7 pkgsrc-2014Q4:1.7.0.24 pkgsrc-2014Q4-base:1.7 pkgsrc-2014Q3:1.7.0.22 pkgsrc-2014Q3-base:1.7 pkgsrc-2014Q2:1.7.0.20 pkgsrc-2014Q2-base:1.7 pkgsrc-2014Q1:1.7.0.18 pkgsrc-2014Q1-base:1.7 pkgsrc-2013Q4:1.7.0.16 pkgsrc-2013Q4-base:1.7 pkgsrc-2013Q3:1.7.0.14 pkgsrc-2013Q3-base:1.7 pkgsrc-2013Q2:1.7.0.12 pkgsrc-2013Q2-base:1.7 pkgsrc-2013Q1:1.7.0.10 pkgsrc-2013Q1-base:1.7 pkgsrc-2012Q4:1.7.0.8 pkgsrc-2012Q4-base:1.7 pkgsrc-2012Q3:1.7.0.6 pkgsrc-2012Q3-base:1.7 pkgsrc-2012Q2:1.7.0.4 pkgsrc-2012Q2-base:1.7 pkgsrc-2012Q1:1.7.0.2 pkgsrc-2012Q1-base:1.7 pkgsrc-2011Q4:1.6.0.8 pkgsrc-2011Q4-base:1.6 pkgsrc-2011Q3:1.6.0.6 pkgsrc-2011Q3-base:1.6 pkgsrc-2011Q2:1.6.0.4 pkgsrc-2011Q2-base:1.6 pkgsrc-2011Q1:1.6.0.2 pkgsrc-2011Q1-base:1.6 pkgsrc-2010Q4:1.5.0.2 pkgsrc-2010Q4-base:1.5 pkgsrc-2010Q3:1.3.0.2 pkgsrc-2010Q3-base:1.3 pkgsrc-2010Q2:1.2.0.2 pkgsrc-2010Q2-base:1.2 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 @# @; 1.7 date 2012.01.14.00.38.18; author asau; state Exp; branches; next 1.6; 1.6 date 2011.03.23.05.36.29; author asau; state Exp; branches; next 1.5; 1.5 date 2010.11.23.19.43.58; author asau; state Exp; branches; next 1.4; 1.4 date 2010.10.21.12.03.57; author asau; state Exp; branches; next 1.3; 1.3 date 2010.09.03.20.52.39; 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 @@ 1.7 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 @@@comment $NetBSD$ bin/GMXRC bin/GMXRC.bash bin/GMXRC.csh bin/GMXRC.zsh bin/completion.bash bin/completion.csh bin/completion.zsh bin/demux.pl bin/do_dssp bin/editconf bin/eneconv bin/g_anadock bin/g_anaeig bin/g_analyze bin/g_angle bin/g_bar bin/g_bond bin/g_bundle bin/g_chi bin/g_cluster bin/g_clustsize bin/g_confrms bin/g_covar bin/g_current bin/g_density bin/g_densmap bin/g_densorder bin/g_dielectric bin/g_dih bin/g_dipoles bin/g_disre bin/g_dist bin/g_dos bin/g_dyndom bin/g_enemat bin/g_energy bin/g_filter bin/g_gyrate bin/g_h2order bin/g_hbond bin/g_helix bin/g_helixorient bin/g_hydorder bin/g_kinetics bin/g_lie bin/g_luck bin/g_mdmat bin/g_membed bin/g_mindist bin/g_morph bin/g_msd bin/g_nmeig bin/g_nmens bin/g_nmtraj bin/g_options bin/g_order bin/g_pme_error bin/g_polystat bin/g_potential bin/g_principal bin/g_protonate bin/g_rama bin/g_rdf bin/g_rms bin/g_rmsdist bin/g_rmsf bin/g_rotacf bin/g_rotmat bin/g_saltbr bin/g_sas bin/g_select bin/g_sgangle bin/g_sham bin/g_sigeps bin/g_sorient bin/g_spatial bin/g_spol bin/g_tcaf bin/g_traj bin/g_tune_pme bin/g_vanhove bin/g_velacc bin/g_wham bin/g_wheel bin/g_x2top ${PLIST.x11}bin/g_xrama bin/genbox bin/genconf bin/genion bin/genrestr bin/gmxcheck bin/gmxdump bin/grompp bin/make_edi bin/make_ndx bin/mdrun bin/mk_angndx ${PLIST.x11}bin/ngmx bin/pdb2gmx bin/tpbconv bin/trjcat bin/trjconv bin/trjorder bin/xplor2gmx.pl bin/xpm2ps include/gromacs/3dview.h include/gromacs/assert.h include/gromacs/atomprop.h include/gromacs/bondf.h include/gromacs/calcgrid.h include/gromacs/calch.h include/gromacs/calcmu.h include/gromacs/centerofmass.h include/gromacs/chargegroup.h include/gromacs/checkpoint.h include/gromacs/confio.h include/gromacs/constr.h include/gromacs/copyrite.h include/gromacs/coulomb.h include/gromacs/dihre.h include/gromacs/displacement.h include/gromacs/disre.h include/gromacs/do_fit.h include/gromacs/domdec.h include/gromacs/domdec_network.h include/gromacs/ebin.h include/gromacs/edsam.h include/gromacs/enxio.h include/gromacs/ffscanf.h include/gromacs/filenm.h include/gromacs/force.h include/gromacs/futil.h include/gromacs/gbutil.h include/gromacs/gen_ad.h include/gromacs/genborn.h include/gromacs/gmx_ana.h include/gromacs/gmx_arpack.h include/gromacs/gmx_blas.h include/gromacs/gmx_cyclecounter.h include/gromacs/gmx_fatal.h include/gromacs/gmx_fft.h include/gromacs/gmx_ga2la.h include/gromacs/gmx_lapack.h include/gromacs/gmx_matrix.h include/gromacs/gmx_parallel_3dfft.h include/gromacs/gmx_random.h include/gromacs/gmx_sort.h include/gromacs/gmx_sse2_double.h include/gromacs/gmx_sse2_single.h include/gromacs/gmx_statistics.h include/gromacs/gmx_system_xdr.h include/gromacs/gmx_wallcycle.h include/gromacs/gmxcomplex.h include/gromacs/gmxcpp.h include/gromacs/gmxfio.h include/gromacs/gpp_atomtype.h include/gromacs/gpp_nextnb.h include/gromacs/grompp.h include/gromacs/gstat.h include/gromacs/hackblock.h include/gromacs/histogram.h include/gromacs/index.h include/gromacs/indexutil.h include/gromacs/inputrec.h include/gromacs/invblock.h include/gromacs/macros.h include/gromacs/magic.h include/gromacs/main.h include/gromacs/mainpage.h include/gromacs/maths.h include/gromacs/matio.h include/gromacs/md5.h include/gromacs/mdatoms.h include/gromacs/mdebin.h include/gromacs/mdrun.h include/gromacs/molfile_plugin.h include/gromacs/mpelogging.h include/gromacs/mshift.h include/gromacs/mtop_util.h include/gromacs/mtxio.h include/gromacs/mvdata.h include/gromacs/names.h include/gromacs/nbsearch.h include/gromacs/network.h include/gromacs/nonbonded.h include/gromacs/nrama.h include/gromacs/nrjac.h include/gromacs/nrnb.h include/gromacs/ns.h include/gromacs/nsgrid.h include/gromacs/oenv.h include/gromacs/orires.h include/gromacs/partdec.h include/gromacs/pbc.h include/gromacs/pdb2top.h include/gromacs/pdbio.h include/gromacs/perf_est.h include/gromacs/physics.h include/gromacs/pme.h include/gromacs/poscalc.h include/gromacs/position.h include/gromacs/pppm.h include/gromacs/princ.h include/gromacs/pull.h include/gromacs/qmmm.h include/gromacs/random.h include/gromacs/rbin.h include/gromacs/rdgroup.h include/gromacs/readinp.h include/gromacs/resall.h include/gromacs/rmpbc.h include/gromacs/selection.h include/gromacs/selmethod.h include/gromacs/selparam.h include/gromacs/selvalue.h include/gromacs/sfactor.h include/gromacs/shellfc.h include/gromacs/shift.h include/gromacs/sighandler.h include/gromacs/smalloc.h include/gromacs/sortwater.h include/gromacs/sparsematrix.h include/gromacs/split.h include/gromacs/splitter.h include/gromacs/statutil.h include/gromacs/strdb.h include/gromacs/string2.h include/gromacs/symtab.h include/gromacs/sysstuff.h include/gromacs/tgroup.h include/gromacs/thread_mpi.h include/gromacs/thread_mpi/atomic.h include/gromacs/thread_mpi/atomic/cycles.h include/gromacs/thread_mpi/atomic/gcc.h include/gromacs/thread_mpi/atomic/gcc_ia64.h include/gromacs/thread_mpi/atomic/gcc_intrinsics.h include/gromacs/thread_mpi/atomic/gcc_ppc.h include/gromacs/thread_mpi/atomic/gcc_spinlock.h include/gromacs/thread_mpi/atomic/gcc_x86.h include/gromacs/thread_mpi/atomic/msvc.h include/gromacs/thread_mpi/atomic/xlc_ppc.h include/gromacs/thread_mpi/barrier.h include/gromacs/thread_mpi/collective.h include/gromacs/thread_mpi/event.h include/gromacs/thread_mpi/list.h include/gromacs/thread_mpi/lock.h include/gromacs/thread_mpi/mpi_bindings.h include/gromacs/thread_mpi/numa_malloc.h include/gromacs/thread_mpi/threads.h include/gromacs/thread_mpi/tmpi.h include/gromacs/thread_mpi/wait.h include/gromacs/tmpi.h include/gromacs/topsort.h include/gromacs/toputil.h include/gromacs/tpxio.h include/gromacs/trajana.h include/gromacs/trnio.h include/gromacs/txtdump.h include/gromacs/typedefs.h include/gromacs/types/atoms.h include/gromacs/types/block.h include/gromacs/types/commrec.h include/gromacs/types/constr.h include/gromacs/types/energy.h include/gromacs/types/enums.h include/gromacs/types/fcdata.h include/gromacs/types/filenm.h include/gromacs/types/forcerec.h include/gromacs/types/genborn.h include/gromacs/types/globsig.h include/gromacs/types/graph.h include/gromacs/types/group.h include/gromacs/types/idef.h include/gromacs/types/ifunc.h include/gromacs/types/inputrec.h include/gromacs/types/ishift.h include/gromacs/types/iteratedconstraints.h include/gromacs/types/matrix.h include/gromacs/types/mdatom.h include/gromacs/types/nblist.h include/gromacs/types/nlistheuristics.h include/gromacs/types/nrnb.h include/gromacs/types/ns.h include/gromacs/types/nsgrid.h include/gromacs/types/oenv.h include/gromacs/types/pbc.h include/gromacs/types/qmmmrec.h include/gromacs/types/shellfc.h include/gromacs/types/simple.h include/gromacs/types/state.h include/gromacs/types/symtab.h include/gromacs/types/topology.h include/gromacs/types/trx.h include/gromacs/update.h include/gromacs/vcm.h include/gromacs/vec.h include/gromacs/viewit.h include/gromacs/vmddlopen.h include/gromacs/vmdio.h include/gromacs/vmdplugin.h include/gromacs/vsite.h include/gromacs/warninp.h include/gromacs/wgms.h include/gromacs/wman.h include/gromacs/writeps.h include/gromacs/xdrf.h include/gromacs/xtcio.h include/gromacs/xvgr.h lib/libgmx${MPI}_d.la lib/libgmxana${MPI}_d.la lib/libgmxpreprocess${MPI}_d.la lib/libmd${MPI}_d.la lib/pkgconfig/libgmx${MPI}_d.pc lib/pkgconfig/libgmxana${MPI}_d.pc lib/pkgconfig/libgmxpreprocess${MPI}_d.pc lib/pkgconfig/libmd${MPI}_d.pc man/man1/do_dssp.1 man/man1/editconf.1 man/man1/eneconv.1 man/man1/g_anadock.1 man/man1/g_anaeig.1 man/man1/g_analyze.1 man/man1/g_angle.1 man/man1/g_bar.1 man/man1/g_bond.1 man/man1/g_bundle.1 man/man1/g_chi.1 man/man1/g_cluster.1 man/man1/g_clustsize.1 man/man1/g_confrms.1 man/man1/g_covar.1 man/man1/g_current.1 man/man1/g_density.1 man/man1/g_densmap.1 man/man1/g_densorder.1 man/man1/g_dielectric.1 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share/gromacs/tutor/water/grompp.mdp share/gromacs/tutor/water/index.ndx share/gromacs/tutor/water/spc216.pdb share/gromacs/tutor/water/topol.top @ 1.6 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 @d1 1 a1 1 @@comment $NetBSD: PLIST,v 1.5 2010/11/23 19:43:58 asau Exp $ d28 1 d34 1 d44 1 a245 1 include/gromacs/thread_mpi/hwinfo.h d249 1 d271 1 d278 1 d282 1 d336 1 d351 1 d361 1 d363 1 d474 1 @ 1.5 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 @d1 1 a1 1 @@comment $NetBSD$ d53 1 @ 1.4 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 @d1 1 a1 1 @@comment $NetBSD: PLIST,v 1.3 2010/09/03 20:52:39 asau Exp $ d42 1 d785 4 d800 5 d810 1 @ 1.3 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 @d1 1 a1 1 @@comment $NetBSD$ d229 1 a235 1 include/gromacs/thread_mpi/atomic/hpux.h @ 1.2 log @Build with MPI support by default. Introduce "mpi" option to turn the above off. 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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 @@