01641df47b
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.
1088 lines
36 KiB
Text
1088 lines
36 KiB
Text
@comment $NetBSD: PLIST,v 1.7 2012/01/14 00:38:18 asau Exp $
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bin/GMXRC
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bin/GMXRC.bash
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bin/GMXRC.csh
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bin/GMXRC.zsh
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bin/completion.bash
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bin/completion.csh
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bin/completion.zsh
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bin/demux.pl
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bin/do_dssp
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bin/editconf
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bin/eneconv
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bin/g_anadock
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bin/g_anaeig
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bin/g_analyze
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bin/g_angle
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bin/g_bar
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bin/g_bond
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bin/g_bundle
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bin/g_chi
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bin/g_cluster
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bin/g_confrms
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bin/g_covar
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bin/g_current
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bin/g_density
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bin/g_densorder
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bin/g_dielectric
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bin/g_dipoles
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bin/g_dist
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bin/g_dyndom
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bin/g_energy
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bin/g_filter
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bin/g_gyrate
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bin/g_h2order
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bin/g_hbond
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bin/g_helix
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bin/g_helixorient
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bin/g_kinetics
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${PLIST.x11}bin/g_xrama
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bin/genbox
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bin/genconf
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bin/genion
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bin/genrestr
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bin/gmxcheck
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bin/gmxdump
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bin/grompp
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bin/make_edi
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bin/make_ndx
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bin/mdrun
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bin/mk_angndx
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${PLIST.x11}bin/ngmx
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bin/pdb2gmx
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bin/tpbconv
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bin/trjconv
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bin/trjorder
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bin/xplor2gmx.pl
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bin/xpm2ps
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include/gromacs/3dview.h
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include/gromacs/assert.h
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include/gromacs/atomprop.h
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include/gromacs/bondf.h
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include/gromacs/calcgrid.h
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include/gromacs/constr.h
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include/gromacs/copyrite.h
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include/gromacs/do_fit.h
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include/gromacs/domdec.h
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include/gromacs/gmx_sse2_double.h
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include/gromacs/gmx_system_xdr.h
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include/gromacs/gmx_wallcycle.h
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include/gromacs/gmxcomplex.h
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include/gromacs/gmxcpp.h
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include/gromacs/gmxfio.h
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include/gromacs/gpp_atomtype.h
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include/gromacs/gpp_nextnb.h
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include/gromacs/grompp.h
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include/gromacs/gstat.h
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include/gromacs/hackblock.h
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include/gromacs/histogram.h
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include/gromacs/index.h
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include/gromacs/indexutil.h
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include/gromacs/inputrec.h
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include/gromacs/invblock.h
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include/gromacs/macros.h
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include/gromacs/magic.h
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include/gromacs/main.h
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include/gromacs/mainpage.h
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include/gromacs/maths.h
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include/gromacs/matio.h
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include/gromacs/md5.h
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include/gromacs/mdatoms.h
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include/gromacs/mdebin.h
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include/gromacs/mdrun.h
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include/gromacs/molfile_plugin.h
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include/gromacs/mpelogging.h
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include/gromacs/mshift.h
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include/gromacs/mtop_util.h
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include/gromacs/mtxio.h
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include/gromacs/mvdata.h
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include/gromacs/names.h
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include/gromacs/nbsearch.h
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include/gromacs/network.h
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include/gromacs/nonbonded.h
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include/gromacs/orires.h
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include/gromacs/pbc.h
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include/gromacs/perf_est.h
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include/gromacs/physics.h
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include/gromacs/poscalc.h
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include/gromacs/pppm.h
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include/gromacs/pull.h
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include/gromacs/qmmm.h
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include/gromacs/sortwater.h
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include/gromacs/sparsematrix.h
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include/gromacs/symtab.h
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include/gromacs/thread_mpi.h
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include/gromacs/thread_mpi/atomic/cycles.h
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include/gromacs/thread_mpi/atomic/gcc.h
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include/gromacs/thread_mpi/atomic/gcc_intrinsics.h
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include/gromacs/thread_mpi/atomic/gcc_spinlock.h
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include/gromacs/thread_mpi/atomic/gcc_x86.h
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include/gromacs/thread_mpi/atomic/msvc.h
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include/gromacs/thread_mpi/atomic/xlc_ppc.h
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include/gromacs/thread_mpi/lock.h
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include/gromacs/thread_mpi/wait.h
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include/gromacs/tmpi.h
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include/gromacs/topsort.h
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include/gromacs/toputil.h
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include/gromacs/tpxio.h
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include/gromacs/trajana.h
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include/gromacs/trnio.h
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include/gromacs/txtdump.h
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include/gromacs/typedefs.h
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include/gromacs/types/atoms.h
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include/gromacs/types/block.h
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include/gromacs/types/commrec.h
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include/gromacs/types/constr.h
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include/gromacs/types/energy.h
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include/gromacs/types/enums.h
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include/gromacs/types/fcdata.h
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include/gromacs/types/filenm.h
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include/gromacs/types/forcerec.h
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include/gromacs/types/genborn.h
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include/gromacs/types/globsig.h
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include/gromacs/types/mdatom.h
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include/gromacs/types/nlistheuristics.h
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include/gromacs/types/nrnb.h
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include/gromacs/types/ns.h
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include/gromacs/types/nsgrid.h
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include/gromacs/types/oenv.h
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include/gromacs/types/pbc.h
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include/gromacs/types/qmmmrec.h
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include/gromacs/types/shellfc.h
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include/gromacs/types/simple.h
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include/gromacs/types/state.h
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include/gromacs/types/symtab.h
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include/gromacs/types/topology.h
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include/gromacs/types/trx.h
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include/gromacs/update.h
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include/gromacs/vcm.h
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include/gromacs/vec.h
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include/gromacs/viewit.h
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include/gromacs/vmddlopen.h
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include/gromacs/vmdio.h
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include/gromacs/vmdplugin.h
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include/gromacs/vsite.h
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include/gromacs/warninp.h
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include/gromacs/wgms.h
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include/gromacs/wman.h
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include/gromacs/writeps.h
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include/gromacs/xdrf.h
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include/gromacs/xtcio.h
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include/gromacs/xvgr.h
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lib/libgmx${MPI}_d.la
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lib/libgmxana${MPI}_d.la
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lib/libgmxpreprocess${MPI}_d.la
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lib/libmd${MPI}_d.la
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lib/pkgconfig/libgmx${MPI}_d.pc
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lib/pkgconfig/libgmxana${MPI}_d.pc
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lib/pkgconfig/libgmxpreprocess${MPI}_d.pc
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lib/pkgconfig/libmd${MPI}_d.pc
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man/man1/do_dssp.1
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man/man1/editconf.1
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man/man1/eneconv.1
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man/man1/g_anadock.1
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man/man1/g_anaeig.1
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man/man1/g_analyze.1
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man/man1/g_angle.1
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man/man1/g_bar.1
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man/man1/g_bond.1
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man/man1/g_bundle.1
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man/man1/g_chi.1
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man/man1/g_cluster.1
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man/man1/g_clustsize.1
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man/man1/g_confrms.1
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man/man1/g_covar.1
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man/man1/g_current.1
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man/man1/g_density.1
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man/man1/g_densmap.1
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man/man1/g_densorder.1
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man/man1/g_dielectric.1
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man/man1/g_dih.1
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man/man1/g_dipoles.1
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man/man1/g_disre.1
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man/man1/g_dist.1
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man/man1/g_dyndom.1
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man/man1/g_enemat.1
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man/man1/g_energy.1
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man/man1/g_filter.1
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man/man1/g_gyrate.1
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man/man1/g_h2order.1
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man/man1/g_hbond.1
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man/man1/g_helix.1
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man/man1/g_helixorient.1
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man/man1/g_hydorder.1
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man/man1/g_lie.1
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man/man1/g_mdmat.1
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man/man1/g_membed.1
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man/man1/g_mindist.1
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man/man1/g_morph.1
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man/man1/g_msd.1
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man/man1/g_nmeig.1
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man/man1/g_nmens.1
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man/man1/g_nmtraj.1
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man/man1/g_options.1
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man/man1/g_order.1
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man/man1/g_pme_error.1
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man/man1/g_polystat.1
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man/man1/g_potential.1
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man/man1/g_principal.1
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man/man1/g_protonate.1
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man/man1/g_rama.1
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man/man1/g_rdf.1
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man/man1/g_rms.1
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man/man1/g_rmsdist.1
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man/man1/g_rmsf.1
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man/man1/g_rotacf.1
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man/man1/g_rotmat.1
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man/man1/g_saltbr.1
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man/man1/g_sas.1
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man/man1/g_select.1
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man/man1/g_sgangle.1
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man/man1/g_sham.1
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man/man1/g_sigeps.1
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man/man1/g_sorient.1
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man/man1/g_spatial.1
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man/man1/g_spol.1
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man/man1/g_tcaf.1
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man/man1/g_traj.1
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man/man1/g_tune_pme.1
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man/man1/g_vanhove.1
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man/man1/g_velacc.1
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man/man1/g_wham.1
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man/man1/g_wheel.1
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man/man1/g_x2top.1
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man/man1/g_xrama.1
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man/man1/genbox.1
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man/man1/genconf.1
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man/man1/genion.1
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man/man1/genrestr.1
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man/man1/gmxcheck.1
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man/man1/gmxdump.1
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man/man1/grompp.1
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man/man1/make_edi.1
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man/man1/make_ndx.1
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man/man1/mdrun.1
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man/man1/mk_angndx.1
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man/man1/ngmx.1
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man/man1/pdb2gmx.1
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man/man1/tpbconv.1
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man/man1/trjcat.1
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man/man1/trjconv.1
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man/man1/trjorder.1
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man/man1/xpm2ps.1
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man/man7/gromacs.7
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share/gromacs/html/gmxfaq.html
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share/gromacs/html/images/1ctf-0.2.jpg
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share/gromacs/html/images/1ctf-0.5.jpg
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share/gromacs/html/images/1ctf-0.jpg
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share/gromacs/top/tip4p.gro
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share/gromacs/top/tip4p.itp
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share/gromacs/top/tip5p.gro
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share/gromacs/top/vdwradii.dat
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share/gromacs/top/xlateat.dat
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share/gromacs/tutor/gmxdemo/cpeptide.pdb
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share/gromacs/tutor/gmxdemo/demo
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share/gromacs/tutor/methanol/conf.gro
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share/gromacs/tutor/methanol/grompp.mdp
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share/gromacs/tutor/methanol/index.ndx
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share/gromacs/tutor/methanol/methanol.itp
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share/gromacs/tutor/methanol/methanol.pdb
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share/gromacs/tutor/methanol/topol.top
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share/gromacs/tutor/mixed/conf.gro
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share/gromacs/tutor/mixed/grompp.mdp
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share/gromacs/tutor/mixed/index.ndx
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share/gromacs/tutor/mixed/mixed.pdb
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share/gromacs/tutor/mixed/topol.top
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share/gromacs/tutor/nmr1/conf.gro
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share/gromacs/tutor/nmr1/grompp.mdp
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share/gromacs/tutor/nmr1/pep.pdb
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share/gromacs/tutor/nmr1/topol.top
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share/gromacs/tutor/nmr2/conf.gro
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share/gromacs/tutor/nmr2/genconf.gcp
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share/gromacs/tutor/nmr2/grompp.mdp
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share/gromacs/tutor/nmr2/pep.pdb
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share/gromacs/tutor/nmr2/topol.top
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share/gromacs/tutor/speptide/em.mdp
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share/gromacs/tutor/speptide/full.mdp
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share/gromacs/tutor/speptide/pr.mdp
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share/gromacs/tutor/speptide/speptide.pdb
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share/gromacs/tutor/water/conf.gro
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share/gromacs/tutor/water/grompp.mdp
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share/gromacs/tutor/water/index.ndx
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share/gromacs/tutor/water/spc216.pdb
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share/gromacs/tutor/water/topol.top
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