Rossen Apostolov [Wed, 15 Dec 2010 10:50:27 +0000 (11:50 +0100)]
Test commit
David van der Spoel [Sat, 11 Dec 2010 20:35:23 +0000 (21:35 +0100)]
Merge branch 'release-4-5-patches'
David van der Spoel [Sat, 11 Dec 2010 20:35:10 +0000 (21:35 +0100)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
David van der Spoel [Sat, 11 Dec 2010 20:34:57 +0000 (21:34 +0100)]
Merge branch 'master' of git.gromacs.org:gromacs
David van der Spoel [Sat, 11 Dec 2010 20:34:46 +0000 (21:34 +0100)]
Merge branch 'release-4-5-patches'
David van der Spoel [Sat, 11 Dec 2010 20:34:05 +0000 (21:34 +0100)]
Added 1 quote.
Pär Bjelkmar [Fri, 10 Dec 2010 12:22:25 +0000 (13:22 +0100)]
Added CHARMM neutral lysine, LYN, to residuetypes.dat.
Christoph Junghans [Fri, 10 Dec 2010 10:11:30 +0000 (11:11 +0100)]
Fixed wrong path ordering in GMX.bash introduced in commit
58a6b0bee590c2293fbf3eb35947005db9f7668b
David van der Spoel [Thu, 9 Dec 2010 11:27:22 +0000 (12:27 +0100)]
Merge branch 'release-4-5-patches'
David van der Spoel [Thu, 9 Dec 2010 11:26:42 +0000 (12:26 +0100)]
Added fatal error for when people use energy files for computing dipoles. This
is broken due to the fact that the dipole is computed based on broken
molecules.
Mark Abraham [Mon, 6 Dec 2010 08:45:32 +0000 (19:45 +1100)]
Added comments and workaround for IBM's BlueGene(/L) MPI_Bcast dereferencing
null pointers even when zero data is to be broadcast. This change will only affect
BlueGene, and does not affect speed of time-critical parts of GROMACS.
Carsten Kutzner [Thu, 2 Dec 2010 14:46:46 +0000 (15:46 +0100)]
Merge branch 'release-4-5-patches'
ckutzne [Thu, 2 Dec 2010 14:44:41 +0000 (15:44 +0100)]
Fixed typo.
Carsten Kutzner [Tue, 30 Nov 2010 12:55:01 +0000 (13:55 +0100)]
Merge branch 'master' of git.gromacs.org:gromacs
ckutzne [Tue, 30 Nov 2010 12:54:21 +0000 (13:54 +0100)]
Proper appending with enforced rotation output files.
Christoph Junghans [Mon, 29 Nov 2010 11:35:18 +0000 (12:35 +0100)]
GMXRC.* - fixed bug #614
Christoph Junghans [Fri, 26 Nov 2010 09:59:54 +0000 (10:59 +0100)]
added power6 flags from Markus Rampp
David van der Spoel [Sun, 28 Nov 2010 10:13:05 +0000 (11:13 +0100)]
Merge branch 'release-4-5-patches'
David van der Spoel [Sun, 28 Nov 2010 10:11:57 +0000 (11:11 +0100)]
Fixed bugzilla 616 about formatting in the help text.
David van der Spoel [Fri, 26 Nov 2010 10:10:18 +0000 (11:10 +0100)]
Fixed SEGV bug in g_sham.
Carsten Kutzner [Fri, 26 Nov 2010 09:31:50 +0000 (10:31 +0100)]
Enforced rotation: fixed torque calculation for FLEX potential when using mass-weighting
Berk Hess [Wed, 24 Nov 2010 12:44:49 +0000 (13:44 +0100)]
fixed segv in grompp due to gmxcpp not checking for #include statements without delimiters
Christoph Junghans [Wed, 24 Nov 2010 08:53:29 +0000 (09:53 +0100)]
configure: build shared libs unless mpi enabled (bug #562)
Carsten Kutzner [Tue, 23 Nov 2010 13:42:33 +0000 (14:42 +0100)]
Merge branch 'master' of git.gromacs.org:gromacs
Carsten Kutzner [Tue, 23 Nov 2010 13:41:15 +0000 (14:41 +0100)]
Enforced rotation: code cleanup
Mark Abraham [Mon, 22 Nov 2010 12:07:47 +0000 (23:07 +1100)]
Added a hint to the documentation for creating .tpr files with a subset of a simulation sustem using tpbconv.
ckutzne [Fri, 19 Nov 2010 17:26:05 +0000 (18:26 +0100)]
Fixed segv in gmx_pme_error when gromacs compiled with threads
Sander Pronk [Fri, 19 Nov 2010 13:38:44 +0000 (14:38 +0100)]
Fixed TMPI_WAIT_FOR_NO_ONE deadlock.
David van der Spoel [Thu, 18 Nov 2010 19:45:00 +0000 (20:45 +0100)]
Made printing in check_multi_init conditional, depending on whether the
log file is NULL or not.
Carsten Kutzner [Thu, 18 Nov 2010 09:09:08 +0000 (10:09 +0100)]
Better description of rotation options
Carsten Kutzner [Wed, 17 Nov 2010 13:02:40 +0000 (14:02 +0100)]
Removed unnecessary include
Carsten Kutzner [Wed, 17 Nov 2010 12:41:08 +0000 (13:41 +0100)]
Merge branch 'rotation'
Carsten Kutzner [Wed, 17 Nov 2010 11:03:56 +0000 (12:03 +0100)]
Merge branch 'release-4-5-patches'
Carsten Kutzner [Mon, 15 Nov 2010 10:30:12 +0000 (11:30 +0100)]
Merge branch 'rotation-4-5' into rotation
Carsten Kutzner [Mon, 15 Nov 2010 10:28:37 +0000 (11:28 +0100)]
Enforced rotation: define Gaussian norm
Carsten Kutzner [Mon, 15 Nov 2010 09:58:10 +0000 (10:58 +0100)]
Merge branch 'rotation-4-5' into rotation
Carsten Kutzner [Mon, 15 Nov 2010 09:56:55 +0000 (10:56 +0100)]
Enforced rotation: use the right tpx_version
Carsten Kutzner [Mon, 15 Nov 2010 09:53:19 +0000 (10:53 +0100)]
Enforced rotation: set the right tpx_version
Carsten Kutzner [Mon, 15 Nov 2010 09:34:52 +0000 (10:34 +0100)]
Merge branch 'release-4-5-patches' into rotation-4-5
Mark Abraham [Fri, 12 Nov 2010 23:03:20 +0000 (10:03 +1100)]
Minor trjconv documentation formatting fix
Mark Abraham [Fri, 12 Nov 2010 23:01:52 +0000 (10:01 +1100)]
g_densmap -od writes a .dat file and prevents writing the .xpm file. The latter behaviour is uncharacteristic of GROMACS tools, I thought, so I updated the documentation to note this. Perhaps the .xpm file produced by -o should always be written.
Rossen Apostolov [Tue, 9 Nov 2010 21:32:11 +0000 (22:32 +0100)]
New maintanance release: 4.5.3
Berk Hess [Tue, 9 Nov 2010 08:47:50 +0000 (09:47 +0100)]
added -resnr option to editconf
Mark Abraham [Tue, 9 Nov 2010 08:16:06 +0000 (19:16 +1100)]
GMX_POWERPC_INVSQRT should be OFF in CMakeLists.txt by default (PowerPC and BlueGene accelerations turn them on, though)
Berk Hess [Tue, 9 Nov 2010 07:49:18 +0000 (08:49 +0100)]
fixed compiler warning in pdb2gmx.c
Rossen Apostolov [Mon, 8 Nov 2010 19:16:09 +0000 (20:16 +0100)]
Reverting back GMX_DLOPEN to default ON
Roland Schulz [Mon, 8 Nov 2010 18:57:01 +0000 (13:57 -0500)]
making error message for vmdio clearer (bug 598)
Pär Bjelkmar [Mon, 8 Nov 2010 16:17:42 +0000 (17:17 +0100)]
Deleted redundant charmm27.ff/dna.r2b.
Rossen Apostolov [Mon, 8 Nov 2010 15:55:22 +0000 (16:55 +0100)]
Disable GMX_DLOPEN by default.
Bug 598 is still open though.
Rossen Apostolov [Mon, 8 Nov 2010 15:45:56 +0000 (16:45 +0100)]
Added support for Altivec kernels on POWERPC.
Hopefully closes bug 573.
Szilard Pall [Mon, 8 Nov 2010 12:49:29 +0000 (13:49 +0100)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Carsten Kutzner [Mon, 8 Nov 2010 10:40:08 +0000 (11:40 +0100)]
Merge branch 'master' into rotation
Conflicts:
src/tools/Makefile.am
Carsten Kutzner [Mon, 8 Nov 2010 10:34:42 +0000 (11:34 +0100)]
Merge branch 'rotation-4-5' into rotation
Carsten Kutzner [Mon, 8 Nov 2010 10:33:26 +0000 (11:33 +0100)]
Enforced rotatin: Put in check for acos value; enhanced output file description
Carsten Kutzner [Mon, 8 Nov 2010 08:58:10 +0000 (09:58 +0100)]
Merge branch 'release-4-5-patches' into rotation-4-5
Mark Abraham [Sun, 7 Nov 2010 01:36:37 +0000 (12:36 +1100)]
Made mdrun exit with a fatal error for EM or NM with -rerun
Mark Abraham [Sat, 6 Nov 2010 11:55:56 +0000 (22:55 +1100)]
Fixed .xvg legends for g_sas options -or and -oa
Szilard Pall [Fri, 5 Nov 2010 22:08:50 +0000 (23:08 +0100)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Teemu Murtola [Fri, 5 Nov 2010 17:53:07 +0000 (19:53 +0200)]
Merge branch 'release-4-5-patches'
Conflicts:
src/tools/Makefile.am
David van der Spoel [Fri, 5 Nov 2010 13:10:25 +0000 (14:10 +0100)]
Fixed compilation issue.
David van der Spoel [Fri, 5 Nov 2010 13:05:55 +0000 (14:05 +0100)]
Fixed compilation issue.
David van der Spoel [Fri, 5 Nov 2010 12:56:06 +0000 (13:56 +0100)]
Added flag to gmx_stats_get_point
Pär Bjelkmar [Fri, 5 Nov 2010 12:38:11 +0000 (13:38 +0100)]
More atom-based charge groups in CHARMM (termini and hard-coded residues).
Carsten Kutzner [Fri, 5 Nov 2010 11:56:31 +0000 (12:56 +0100)]
Merge branch 'rotation-4-5' into rotation
Carsten Kutzner [Fri, 5 Nov 2010 11:55:44 +0000 (12:55 +0100)]
Flexible RMSD fitting is now optionally mass-weighted
Carsten Kutzner [Fri, 5 Nov 2010 10:02:06 +0000 (11:02 +0100)]
Print warning when reference file is set but could not be found
Berk Hess [Fri, 5 Nov 2010 09:18:29 +0000 (10:18 +0100)]
pdb2gmx now puts atoms with cgnr=-1 in separate charge groups
Carsten Kutzner [Fri, 5 Nov 2010 08:54:34 +0000 (09:54 +0100)]
Merge branch 'release-4-5-patches' into rotation-4-5
Roland Schulz [Thu, 4 Nov 2010 08:14:56 +0000 (04:14 -0400)]
print more information in case of lock error
Carsten Kutzner [Thu, 4 Nov 2010 10:51:56 +0000 (11:51 +0100)]
Merge branch 'rotation-4-5' into rotation
Conflicts:
src/tools/Makefile.am
Carsten Kutzner [Thu, 4 Nov 2010 10:45:40 +0000 (11:45 +0100)]
Doxygen comment for dd_make_local_rotation_groups
Berk Hess [Thu, 4 Nov 2010 10:19:35 +0000 (11:19 +0100)]
Fixed md.log being opened twice when appending, which prevented file locking.
Added check for -seppot and -append.
Carsten Kutzner [Thu, 4 Nov 2010 09:42:45 +0000 (10:42 +0100)]
Merge branch 'master' into rotation
Conflicts:
src/kernel/runner.c
Carsten Kutzner [Thu, 4 Nov 2010 09:33:40 +0000 (10:33 +0100)]
Merge branch 'release-4-5-patches' into rotation-4-5
Carsten Kutzner [Thu, 4 Nov 2010 09:31:24 +0000 (10:31 +0100)]
Merge branch 'rotation-4-5' into rotation
Carsten Kutzner [Thu, 4 Nov 2010 09:28:38 +0000 (10:28 +0100)]
Updated normalization factor
hess [Thu, 4 Nov 2010 08:42:54 +0000 (09:42 +0100)]
added GB params for charmm MCH3S
hess [Thu, 4 Nov 2010 08:42:18 +0000 (09:42 +0100)]
clarified GB parameter error messages in grompp
Szilard Pall [Wed, 3 Nov 2010 11:32:52 +0000 (12:32 +0100)]
now it's possible to run binaries in the build tree (fixes bug #570)
Changed CMAKE_BUILD_WITH_INSTALL_RPATH to FALSE which results in the
rpath being rewritten on while installing binaries. CPack also works.
Berk Hess [Tue, 2 Nov 2010 17:29:26 +0000 (18:29 +0100)]
fixed incorrect print in fatal error on charge group size
Berk Hess [Tue, 2 Nov 2010 17:16:13 +0000 (18:16 +0100)]
proper defined of MAX_CHARGEGROUP_SIZE=32 in a single include file
David van der Spoel [Tue, 2 Nov 2010 15:09:35 +0000 (16:09 +0100)]
Fixed bug 608 by throwing a fatal error in grompp.
Sander Pronk [Tue, 2 Nov 2010 12:27:01 +0000 (13:27 +0100)]
Fixed double precision energy file reading + box matrix writing to ener.edr
- double precision energy files can now be read back
- All non-zero elements of the box matrix are now correctly written out
when needed
hess [Tue, 2 Nov 2010 07:50:33 +0000 (08:50 +0100)]
fixed incorrect y result in mvmul_ur0, only used in g_vanhove
Rossen Apostolov [Sat, 30 Oct 2010 20:07:36 +0000 (22:07 +0200)]
Added back the "-dev" suffixes to the version strings.
Rossen Apostolov [Sat, 30 Oct 2010 19:22:54 +0000 (21:22 +0200)]
New bugfix release: 4.5.2
Rossen Apostolov [Sat, 30 Oct 2010 17:27:54 +0000 (19:27 +0200)]
For MPI builds, CMake will first try to compile a sample MPI program.
On some systems such as Cray the FindMPI.cmake module can't find the proper
libraries to link to. Therefore we now test whether the given C compiler
is an MPI wrapper and skip the rest of the tests.
Thanks to Roland Schulz for the patch.
Sander Pronk [Sat, 30 Oct 2010 15:11:18 +0000 (17:11 +0200)]
Added Windows macro for snprintf.
Rossen Apostolov [Fri, 29 Oct 2010 19:24:17 +0000 (21:24 +0200)]
added g_kinetics to the CMake build scripts
Szilard Pall [Fri, 29 Oct 2010 17:06:10 +0000 (19:06 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Szilard Pall [Fri, 29 Oct 2010 17:04:44 +0000 (19:04 +0200)]
enabled GMX_PREFER_STATIC_LIBS CMake option for CYGWIN
As it turns out that Cygwin also uses ".a" for static libraries,
the it is safe to enable this option.
Carsten Kutzner [Fri, 29 Oct 2010 16:38:33 +0000 (18:38 +0200)]
Fixed segv in gmx_hbond
Szilard Pall [Fri, 29 Oct 2010 15:24:06 +0000 (17:24 +0200)]
fixed the default for OpenMM plugin dir location (bug #606)
The OpenMM plugin lookup mechanism works again, so when running mdrun-gpu
on the same machine/OS where the binaries were built, the plugins are picked
up from the OpenMM installation used for building (but the env.var.
OPENMM_PLUGIN_DIR still has priority over all defaults!).
Szilard Pall [Fri, 29 Oct 2010 15:28:02 +0000 (17:28 +0200)]
fixed make install-mdrun issue (bug #605)
Szilard Pall [Fri, 29 Oct 2010 14:18:01 +0000 (16:18 +0200)]
(re)added "-dev" suffix for the CMake hardcoded version number
This avoids the potential confusion when the source from a git
release banch is used on machines without git. In these cases the
version reported by gromacs binaries would be the same as the
version of an official release, while former might actually
differ from the release in some patches from git.
Szilard Pall [Fri, 29 Oct 2010 13:44:31 +0000 (15:44 +0200)]
added CMake option GMX_PREFER_STATIC_LIBS (also fixes bug #541)
This option instructs CMake to prefer static external libs when both static
and shared version available. This makes possible linking statically against
external libraries (e.g. fftw, xml2).
The option only available on *NIX platforms, except APPLE and CYGWIN.
Note, that when the option is enabled UILD_SHARED_LIBS gets disabled.
Also note, that with this option on, the binaries built will still be
dynamically linked against system libraries.
David van der Spoel [Thu, 28 Oct 2010 20:26:28 +0000 (22:26 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
David van der Spoel [Thu, 28 Oct 2010 20:23:45 +0000 (22:23 +0200)]
Fixed bug 604 as requested.
Per Larsson [Thu, 28 Oct 2010 18:44:59 +0000 (20:44 +0200)]
Fixed a bug in the all-vs-all sse gb kernels, where an exclusion mask was
calculated incorrectly. Also fixes to loop indeces in the all-vs-all non-sse
code.
Berk Hess [Thu, 28 Oct 2010 10:12:24 +0000 (12:12 +0200)]
added HEM to HEME renaming for Gromos and Charmm ff's