Carsten Kutzner [Fri, 9 Mar 2012 09:10:17 +0000 (10:10 +0100)]
Merge "Improved warning note with DD and periodic molecules" into release-4-5-patches
Mark Abraham [Fri, 9 Mar 2012 02:22:22 +0000 (13:22 +1100)]
Editorial changes to tools documentation
Made LaTeX type-setting of maths in documentation of tools more
sophisticated, without changing the presentation of maths in
plain text mode.
Various spelling and typographical fixes also.
Change-Id: Ia0c13e1f2ba825911c6e0673af6b940aba9efa21
Mark Abraham [Thu, 8 Mar 2012 22:10:51 +0000 (09:10 +1100)]
Improved warning note with DD and periodic molecules
Change-Id: I3f7f201edcce1b70a360d0462e5103dfc144b2d7
David van der Spoel [Thu, 8 Mar 2012 07:28:30 +0000 (08:28 +0100)]
Merge "Minimal support for Clang" into release-4-5-patches
Berk Hess [Mon, 5 Mar 2012 11:18:58 +0000 (12:18 +0100)]
fixed g_anaeig incorrect multiple extremes, fixes #870
Change-Id: Id06f267c1da300f2a940778833ec35b85fecd3f1
Berk Hess [Mon, 5 Mar 2012 10:57:22 +0000 (11:57 +0100)]
added check for mass-weighting with g_anaeig -entropy, fixes #785
Change-Id: I7a1623ba7a7c7987078901876fb4717d8c0a7261
Berk Hess [Mon, 5 Mar 2012 10:43:48 +0000 (11:43 +0100)]
removed initial temperature with OpenMM, fixes #757
Change-Id: Ifc661ce3ece3dfcd2e4bad862392b96d64e70c18
Roland Schulz [Sat, 3 Mar 2012 20:16:03 +0000 (15:16 -0500)]
Minimal support for Clang
Change-Id: I4c6fb22ef8b5d596527eb8fe0991c3c573be606c
Berk Hess [Mon, 27 Feb 2012 14:05:25 +0000 (15:05 +0100)]
fixed array index out of bounds in EM force trr storage
The partially implemented force copy was a leftover from a different way
of copying, which should never have been committed.
Change-Id: I026aa79158afcc327185f2f0cf6167d040eccede
David van der Spoel [Sat, 25 Feb 2012 13:36:54 +0000 (14:36 +0100)]
Merge "Minor formatting fixes to .mdp option documentation" into release-4-5-patches
Mark Abraham [Fri, 24 Feb 2012 00:29:21 +0000 (11:29 +1100)]
Minor formatting fixes to .mdp option documentation
Change-Id: I71762463880e4cb650f680a2ed83125e450f003a
Mark Abraham [Tue, 21 Feb 2012 06:03:39 +0000 (17:03 +1100)]
Fix pdb2gmx -cmap in corner cases
CMAP torsions are only generated when the atoms are from the same chain
(pdb2gmx -merge allows multiple chains to be present in the
moleculetype), and their residues are in residuetypes.dat as
"Protein".
Fixes #800, #885
Change-Id: Idc4f9a867beedc0be6a4c153606c0731eec86f5f
Sander Pronk [Wed, 22 Feb 2012 08:01:19 +0000 (09:01 +0100)]
Fixed ABI warning for thread_mpi on gcc 4.6 for x86.
Atomic operation data structures are now padded to the size of a cache
line instead of aligned to the start of a cache line. This works just
as well, but eliminates a warning in gcc 4.6.
Change-Id: I8d00778dcfea41cdb518b083a9c0732e8d978c66
Teemu Murtola [Tue, 21 Feb 2012 18:52:10 +0000 (19:52 +0100)]
Merge "Use Git server (mirror) to avoid fetching problems" into release-4-5-patches
Roland Schulz [Tue, 21 Feb 2012 04:37:26 +0000 (23:37 -0500)]
Use Git server (mirror) to avoid fetching problems
Change-Id: I144082bd01cf6a5f0583feac0e7877e8e1b163ff
Sander Pronk [Mon, 13 Feb 2012 17:28:56 +0000 (18:28 +0100)]
Fixed an allocation issue with dH histograms.
Change-Id: Ifc6ed94d77664e3b3afb7fe8dbd1016444d86bc3
Szilárd Páll [Sat, 11 Feb 2012 16:45:25 +0000 (17:45 +0100)]
Merge changes If0c2f9d9,Ic2a8ad82 into release-4-5-patches
* changes:
Fixed g_sham using more than three dimensions
Integer multiplication that checks for overflow
Mark Abraham [Thu, 9 Feb 2012 02:48:35 +0000 (13:48 +1100)]
Fixed g_sham using more than three dimensions
When the value given with g_sham -n was greater than 3, arrays used to
overflow and pick_minima() did not work. pick_minima() has been updated
to treat an arbitrary number of dimensions, but retains the particular
code for the two- and three-dimensional cases in the hope that these
are faster. The logic of the complex conditionals has hopefully been
made easier to follow without compromising performance with modern
compilers. Index variables are now of gmx_large_int_t type, as
high-dimensional cases can have large numbers of grid points very fast.
Change-Id: If0c2f9d9ceaf2b5c4c8b1a28a942fae8349fb600
Mark Abraham [Fri, 10 Feb 2012 04:10:34 +0000 (15:10 +1100)]
Integer multiplication that checks for overflow
Integer multiplication overflows silently in C, and sometimes we need to
know when it would. For example, when computing the size of
multi-dimensional arrays, we can need to manage the case when the number
of dimensions and their size is too large to represent in the available
type.
Change-Id: Ic2a8ad820838cf314bb985511e483fc397ba35e2
Christoph Junghans [Fri, 10 Feb 2012 01:14:01 +0000 (02:14 +0100)]
Merge "Fixed bug with COM motion removal on part of the system" into release-4-5-patches
Berk Hess [Mon, 6 Feb 2012 18:57:50 +0000 (19:57 +0100)]
Fixed bug with COM motion removal on part of the system
Center of mass motion removal on one group (not multiple) which is only part
of system would result in a tpr file with COM removal on the whole system.
Fixes #881
Change-Id: I181427bcad237045060000908f2c28d6e97c1ea4
Roland Schulz [Sat, 4 Feb 2012 20:18:24 +0000 (15:18 -0500)]
Fix ICC on Windows Build
Fix NASM with NMake Generator
The workaround in parser.y may not be necessary any longer when this is
merged into master.
Change-Id: I810eec3fa4a13fd912da3832279e8ab47a62bdec
Szilárd Páll [Thu, 2 Feb 2012 23:04:07 +0000 (00:04 +0100)]
Merge "Append all ICC Performance flags only to Release Flags" into release-4-5-patches
Teemu Murtola [Thu, 2 Feb 2012 16:10:18 +0000 (17:10 +0100)]
Merge "Revert "Fix ICC on Windows Build"" into release-4-5-patches
David van der Spoel [Wed, 1 Feb 2012 08:10:58 +0000 (09:10 +0100)]
Merge "Fixed error message to identify the correct file" into release-4-5-patches
David van der Spoel [Wed, 1 Feb 2012 07:58:54 +0000 (08:58 +0100)]
Merge "Fixed trjconv -sub" into release-4-5-patches
David van der Spoel [Wed, 1 Feb 2012 07:57:14 +0000 (08:57 +0100)]
Merge "Improved error message" into release-4-5-patches
Mark Abraham [Wed, 1 Feb 2012 05:57:08 +0000 (16:57 +1100)]
Fixed trjconv -sub
If the index group contains 1..100, then clust->maxframe == 99,
and thus when frame == clust->maxframe it should be included
in the cluster.
Change-Id: I6e093d9f76d0952b31ea9ee1516bade9e9b4419b
Mark Abraham [Wed, 1 Feb 2012 04:45:41 +0000 (15:45 +1100)]
Fixed error message to identify the correct file
When a frame exists, that file has *not* run out of frames.
Change-Id: Ief52d5a17ef73ab318f6d8e00d1f5acb71b69f52
Christoph Junghans [Wed, 1 Feb 2012 04:52:29 +0000 (05:52 +0100)]
Merge "Fix signed/unsigned warnings" into release-4-5-patches
Mark Abraham [Tue, 31 Jan 2012 13:43:18 +0000 (00:43 +1100)]
Improved error message
Users would be confused by "Atom N3 is used in an interaction of
type atom in the topology database..." so when "atom" is the
bondtype we don't mention the fact.
Also changed variable name from bDontQuit to bAllowMissing for
consistency with variable names used in pdb2gmx when calling
this code.
Change-Id: Ie8cb3ba64f39d3746b470fa6ae44f5a6f4b6a16c
Roland Schulz [Tue, 31 Jan 2012 23:47:52 +0000 (00:47 +0100)]
Revert "Fix ICC on Windows Build"
This reverts commit
e8e495fe4317c2e489acb4e82e004afdac618e92
Roland Schulz [Tue, 31 Jan 2012 11:01:29 +0000 (06:01 -0500)]
Append all ICC Performance flags only to Release Flags
Some of the ICC performance flags were appended to GMXC_CFLAGS
and thus also used e.g. for Debug.
Change-Id: Iadfaa29fb347f24208e6f2406e0d1ad41f037804
David van der Spoel [Tue, 31 Jan 2012 18:38:42 +0000 (19:38 +0100)]
Merge "Fix ICC on Windows Build" into release-4-5-patches
Mark Abraham [Tue, 31 Jan 2012 13:51:19 +0000 (14:51 +0100)]
Merge "Corrected use of ?: in conditional" into release-4-5-patches
Roland Schulz [Mon, 30 Jan 2012 07:34:03 +0000 (02:34 -0500)]
Fix signed/unsigned warnings
Change-Id: I3318f06f303a08068849d820381e99267543b4f5
Mark Abraham [Tue, 31 Jan 2012 07:10:55 +0000 (18:10 +1100)]
Made error message even more explicit
Change-Id: Ib1f2e01ca24c5fb305fe220e34797d6991c3f080
Roland Schulz [Mon, 30 Jan 2012 07:11:48 +0000 (02:11 -0500)]
Fix ICC on Windows Build
The workaround in parser.y may not be necessary any longer when this is
merged into master.
Change-Id: I48199b55ede5d786a69c41ab008ef3055101d3b0
Mark Abraham [Tue, 31 Jan 2012 05:20:16 +0000 (16:20 +1100)]
Corrected use of ?: in conditional
Patch contributed by Matthew Zwier to fix the incorrect use of
precedence of ?: and != operators.
Fixes #872
Change-Id: Ie4bbc3cbdaf33fc0386d12c2e142a9c076c2e946
Roland Schulz [Wed, 25 Jan 2012 18:36:49 +0000 (19:36 +0100)]
Merge "New approach for GerritBuild script" into release-4-5-patches
David van der Spoel [Fri, 20 Jan 2012 08:15:33 +0000 (09:15 +0100)]
Merge "Fixed timing measurements." into release-4-5-patches
Roland Schulz [Wed, 18 Jan 2012 09:21:18 +0000 (04:21 -0500)]
New approach for GerritBuild script
- Allows to make changes to build in seperate RelEng repository
- Replaces Matrix view by a linear list of configurations
Change-Id: I7f5c76805836c4cd06527b949ab7ac68f27a31b5
Szilard Pall [Mon, 16 Jan 2012 20:46:59 +0000 (21:46 +0100)]
Fixed timing measurements.
With the VV integrator, kinetic energy calculations are done before the
main MD loop. These should be excluded from the timing measurements.
Change-Id: Ib06b1154965735adc0ff2e20802f78d96ed6fca4
Sander Pronk [Mon, 16 Jan 2012 16:50:42 +0000 (17:50 +0100)]
Thread affinity and x86 assembly fixes for thread_mpi
set_affinity_np now fails silently (shouldn't do much on recent linux
systems, anyway)
x86 asm changes for llvm compatibility.
Change-Id: Id1e71d3e693bc39f5a5e84b0e949fb41c7b7d0e3
Christoph Junghans [Sun, 15 Jan 2012 01:47:41 +0000 (02:47 +0100)]
Merge "Added CMake Toolchain file for BlueGene/P" into release-4-5-patches
Mark Abraham [Wed, 4 Jan 2012 03:47:05 +0000 (14:47 +1100)]
Fixed use of isfinite and _isfinite
Implemented proper CMake tests for the above functionality.
Catered for MSVC idiosyncratic _finite() function. Removed
erroneous use of HAS_ISFINITE and HAS__ISFINITE.
Encapsulated the use of preprocessor directives into the new
gmx_isfinite() function so the programmer doesn't need to
know about the foregoing mess.
The previous versions resulted in unreachable code.
Change-Id: I7471388ed8f402c3f8b664e7846465de4b85f578
Christoph Junghans [Wed, 4 Jan 2012 15:52:39 +0000 (16:52 +0100)]
Merge "Documented the function of g_cluster -cl -noav" into release-4-5-patches
David van der Spoel [Wed, 4 Jan 2012 09:58:22 +0000 (10:58 +0100)]
Introduced fatal error in grompp for incorrect use of settle and charge groups.
Change-Id: I02dfe3f3454a6fc329d9b5ecb2fd4b544c8d2cd1
Mark Abraham [Fri, 16 Dec 2011 04:02:52 +0000 (15:02 +1100)]
Added CMake Toolchain file for BlueGene/P
Change-Id: Iff9b5fe3cccc4d18fc252856a1b50ee64630b54a
Mark Abraham [Thu, 29 Dec 2011 22:39:34 +0000 (09:39 +1100)]
Documented the function of g_cluster -cl -noav
A definition was needed for the center of a cluster.
Change-Id: Id1c6d2f229feb27b7981c2d616e78e510d215a9a
Roland Schulz [Tue, 27 Dec 2011 09:29:19 +0000 (10:29 +0100)]
Merge "Added -dhdl to tpr file list, fixes #855" into release-4-5-patches
Carsten Kutzner [Mon, 19 Dec 2011 14:42:29 +0000 (15:42 +0100)]
Added -dhdl to tpr file list, fixes #855
Change-Id: I2621c7bb44daa01e25831e2d44c22cdcf47f58e7
Roland Schulz [Tue, 20 Dec 2011 07:52:33 +0000 (08:52 +0100)]
Merge "Using MinSizeRel configuration and Release target on Windows" into release-4-5-patches
Roland Schulz [Tue, 20 Dec 2011 07:52:06 +0000 (08:52 +0100)]
Merge changes Iaf4c56b7,Ibabed87f into release-4-5-patches
* changes:
Testing external BLAS/LAPACK
Using 2 cores per build on Windows
Christoph Junghans [Mon, 19 Dec 2011 18:23:25 +0000 (11:23 -0700)]
Set GMX_*_ASM true if GMX_ACCELERATION != auto
In case GMX_ACCELERATION was set to SSE manually (like in Gentoo Linux)
GMX_*_ASM would never be set (false), so sse kernel will not be build.
Change-Id: Icf04707c6174a0182fe4472536b568e1d2d91166
Roland Schulz [Thu, 15 Dec 2011 12:01:55 +0000 (07:01 -0500)]
Using MinSizeRel configuration and Release target on Windows
Faster build:
no need to compute debug symbols
dynamic library
low optimization level
Also fixing MSVC warnings with this configuration
Change-Id: Ic87da40f1e78e2ac70ef543525b49f4cf1a3f639
Roland Schulz [Thu, 15 Dec 2011 08:20:17 +0000 (03:20 -0500)]
Testing external BLAS/LAPACK
Change-Id: Iaf4c56b7e62654425801cd8d3272c4028b016a2a
Roland Schulz [Thu, 15 Dec 2011 06:27:08 +0000 (01:27 -0500)]
Using 2 cores per build on Windows
Windows build is much slower than Linux build. Don't understand why
but hopefully using 2 cores will help narrow that gap.
Change-Id: Ibabed87f2f4d6c931fbb1ebd25c571be9a2cb9ee
Roland Schulz [Wed, 14 Dec 2011 01:49:28 +0000 (02:49 +0100)]
Merge "Re-fixed static linking of maths libraries under UNIX" into release-4-5-patches
Mark Abraham [Wed, 14 Dec 2011 01:10:26 +0000 (12:10 +1100)]
Re-fixed static linking of maths libraries under UNIX
In commit
5e51ffa9 I submitted a patch for the above case, and
suggested the same to CMake. The CMake developers have refined
this and I'm back-porting their fix here.
See http://public.kitware.com/Bug/view.php?id=12477 for details
Change-Id: Ib48bc6b5a87b66b51c893e24aa42e4cd4db32a38
Roland Schulz [Tue, 13 Dec 2011 02:04:29 +0000 (03:04 +0100)]
Merge "Relaxed some assumptions about trajectory times" into release-4-5-patches
Mark Abraham [Tue, 13 Dec 2011 00:04:04 +0000 (11:04 +1100)]
Relaxed some assumptions about trajectory times
Counting of dihedral transitions used to assume that each frame was
equally spaced in time. This is only necessary for making a
subsequent histogram of those transition times (unless more
elaborate machinery was written for that histogram).
Also documented what g_angle -ot and -oh do.
Change-Id: I587dba94c40a1a69e5aa227d09271166db055595
Roland Schulz [Sun, 11 Dec 2011 19:47:54 +0000 (20:47 +0100)]
Merge "Set -DMPI only if compiled for FAH" into release-4-5-patches
Roland Schulz [Sun, 11 Dec 2011 18:51:07 +0000 (13:51 -0500)]
Set -DMPI only if compiled for FAH
MPI conflicts with C++ MPI namespace.
This allows to compile with FAH or with C++ and MPI.
Compiling with FAH and C++ and MPI will still have a name conflict.
Resolves #849
Change-Id: I73ccb7b0e682ae6d12352c76e26c6d79e93ea798
Roland Schulz [Sun, 11 Dec 2011 02:35:47 +0000 (21:35 -0500)]
Fixing MSVC unsigned/signed warnings
Change-Id: I110b591cfd8c8078f3b7853bdf2db6a705e9e453
Roland Schulz [Sat, 10 Dec 2011 00:53:12 +0000 (19:53 -0500)]
Run tests also on Windows
Change-Id: Iab166b5cc8e394e3d330afffd86aced00aa7e0a2
Roland Schulz [Tue, 11 Oct 2011 21:32:42 +0000 (17:32 -0400)]
Only check those atoms for PBC which are part of selection (Issue #809)
Change-Id: I2afccb82c3b761890f4d1f53d842606bb8404c98
Roland Schulz [Thu, 8 Dec 2011 19:57:05 +0000 (20:57 +0100)]
Merge "Fix selection parsing in double precision." into release-4-5-patches
Roland Schulz [Thu, 8 Dec 2011 19:53:08 +0000 (20:53 +0100)]
Merge "Avoid possible warnings if HUGE_VAL != infinity." into release-4-5-patches
Roland Schulz [Fri, 2 Dec 2011 21:48:17 +0000 (16:48 -0500)]
Adding support for Windows build and different CMake Versions
Ant doesn't work very well - trying shell script instead
Change-Id: Ia08e6979c0e0734c33183840c9d34c3a7367af4a
Teemu Murtola [Thu, 1 Dec 2011 16:00:09 +0000 (18:00 +0200)]
Fix selection parsing in double precision.
Fixes #850.
Change-Id: Ifd0bf1f5401ca4d62571c8c2fc39e67cac537ecf
Teemu Murtola [Thu, 1 Dec 2011 15:52:28 +0000 (17:52 +0200)]
Avoid possible warnings if HUGE_VAL != infinity.
Replaced HUGE_VAL by GMX_REAL_MAX in one source file for trajectory
analysis library source file, since it seemed to cause compiler warnings
on some systems.
Reported by Chris Neale on gmx-users.
Change-Id: Ic52a01c5bcedb244d1453117f626ef4f0d46df78
Roland Schulz [Wed, 30 Nov 2011 10:10:25 +0000 (05:10 -0500)]
Adding Gerrit Build description
Change-Id: Ib9e88333967178c8f0962a72e5f8432067094e77
Roland Schulz [Sun, 27 Nov 2011 21:30:25 +0000 (16:30 -0500)]
Removing TestBuildAll test
No need for it because ctest automtically tests building anyhow
It does not work under Windows (using msbuild not make)
Change-Id: I02c7152d61cbe5b536c86c406f37ed78db94ee11
Roland Schulz [Mon, 28 Nov 2011 02:47:22 +0000 (21:47 -0500)]
Fix FFTW API usage
FFTW API uses the fftw/fftwf prefix to select the precision.
To make the code indepent Gromacs uses the FFTW macro.
In this case the marco wasn't used but it had no effect
because for iodim both version are identical.
Submitted by Ake Sandgren (ake.sandgren@hpc2n.umu.se) to gmx-developers
Change-Id: I8ad037b90caef5952b7b49379b81b2c8e90b0daa
Roland Schulz [Sun, 27 Nov 2011 21:48:33 +0000 (22:48 +0100)]
Merge "Initialize variables to make GCC 4.6 not complain" into release-4-5-patches
Berk Hess [Sun, 27 Nov 2011 21:29:35 +0000 (22:29 +0100)]
fixed pull constraint periodicity consistency check, fixes #844
Change-Id: Ifb8e37c5ca3bb5c36631c0b3db65928f27887bdb
Roland Schulz [Thu, 24 Nov 2011 06:03:50 +0000 (01:03 -0500)]
Initialize variables to make GCC 4.6 not complain
The variables are only used when initialized but GCC doesn't detect that.
Change-Id: Ib79383e14d5de90f99f0f267e5039f811980bdb8
Mark Abraham [Wed, 23 Nov 2011 03:19:17 +0000 (14:19 +1100)]
Only analyse angle transitions for dihedral angles
Change-Id: Ia973d5b31c38f94a7ca2e3c2d8265b3552253103
Roland Schulz [Thu, 24 Nov 2011 00:20:03 +0000 (01:20 +0100)]
Merge "Fixed g_angle -f -or to copy times from -f to -or" into release-4-5-patches
Mark Abraham [Tue, 24 Nov 2009 02:10:17 +0000 (15:10 +1300)]
Added protective preprocessor directives
Avoids code compiled with -O0 dereferencing null pointers. Duplicates
and expands a fix suggested by Valentin Pavlov <x.pavlov@gmail.com>.
Change-Id: I41f27bce385c5f960270ac616abd6fdd038312fa
Mark Abraham [Wed, 23 Nov 2011 01:46:05 +0000 (12:46 +1100)]
Fixed g_angle -f -or to copy times from -f to -or
Change-Id: Ie3d45c7454880cf65d583980cf6639f5527b22c9
Carsten Kutzner [Tue, 22 Nov 2011 14:14:48 +0000 (15:14 +0100)]
Actually -cpi and -bcpo must not be identical
Change-Id: Iac44c2dc7d7add1f951ff6018bbfaabe8160af25
Berk Hess [Tue, 15 Nov 2011 14:14:45 +0000 (15:14 +0100)]
fixed dd load print frequency with nsteps=-1, fixes #829
Change-Id: I66736af49665e6cc90875acbf52a45b5a9727915
Christoph Junghans [Tue, 8 Nov 2011 03:18:08 +0000 (04:18 +0100)]
Merge "Fixed bug #830 (segv in do_dssp)" into release-4-5-patches
Kasson [Tue, 8 Nov 2011 02:47:36 +0000 (03:47 +0100)]
Merge "Fix for GB, double, SSE2 and optimized kernels" into release-4-5-patches
Mark Abraham [Wed, 2 Nov 2011 05:00:18 +0000 (16:00 +1100)]
Fix for GB, double, SSE2 and optimized kernels
As suggested by Julius Su in
http://lists.gromacs.org/pipermail/gmx-developers/2011-November/005432.html
Change-Id: Id50d63958e8b3fee810a8d4ed6e021510c98d9aa
Mark Abraham [Tue, 1 Nov 2011 15:41:04 +0000 (02:41 +1100)]
Trigger correct kernels under Cygwin
CMAKE_SYSTEM_PROCESSOR calls uname -p, which returns "unknown" on
Cygwin, so we need to use another mechanism to trigger the use of
SSE/SSE2 optimization.
Change-Id: Ic6406bb36b853a2bd3b22345e36e4914eb04fd8d
Carsten Kutzner [Mon, 31 Oct 2011 10:52:33 +0000 (11:52 +0100)]
Fixed bug #830 (segv in do_dssp)
Change-Id: Ibaa2cf25586d879fce62e9086fee1b510e034e40
Mark Abraham [Thu, 27 Oct 2011 06:34:37 +0000 (17:34 +1100)]
Made reading of binary matrices more robust
The routine to read the binary matrix should check that the storage is
available before using it. Also, the documentation in the header
should be explicit that valid storage locations need to be passed in.
Change-Id: I95e9120bceac02031a7f39412ba226ef2644a444
Christoph Junghans [Thu, 20 Oct 2011 12:14:49 +0000 (14:14 +0200)]
Merge "Fixes for GB kernel" into release-4-5-patches
Teemu Murtola [Wed, 19 Oct 2011 15:30:38 +0000 (17:30 +0200)]
Merge "fixed pull constraining doing nothing, fixes #825" into release-4-5-patches
Mark Abraham [Wed, 19 Oct 2011 11:59:48 +0000 (22:59 +1100)]
Corrected charge of CHARMM zinc ion to +2
Change-Id: Id64c3f5bbd9e0993e4b598dc971a780d3d7337dc
Roland Schulz [Fri, 14 Oct 2011 03:28:10 +0000 (23:28 -0400)]
call to gmx_mtop_generate_local_top is only required once
fixes memory leak
Change-Id: I1ef9860e4b5c24a15acd1b2de88d89721771d840
Berk Hess [Thu, 13 Oct 2011 08:16:11 +0000 (10:16 +0200)]
fixed pull constraining doing nothing, fixes #825
Change-Id: Iefadc0bb34241f91998e6d9f974150da54397045
Berk Hess [Thu, 6 Oct 2011 14:55:30 +0000 (16:55 +0200)]
fixed segv in parallel replica exchange
The last fix and commit of mdrun.c, ea3111, caused a segv with multisim
when the simulations were in parallel. Fixes #821
Change-Id: Ie3936b224d81dc3a304357bcd3438d2b4f5192e3
Mark Abraham [Thu, 6 Oct 2011 12:20:13 +0000 (23:20 +1100)]
Removed erroneous use of MASSV on BlueGene
MASSV does not provide BLAS or LAPACK (indeed, there is no standard
version for BlueGene), and is not useful otherwise. So it was erroneous
to require BLAS and LAPACK, and not helpful to link to MASSV.
Change-Id: I9b82875e9c6b02800e1ec6330f2a9006a563719d
Mark Abraham [Mon, 23 Nov 2009 02:17:06 +0000 (15:17 +1300)]
Fixes for GB kernel
Change-Id: I9108b02d032b6c7779c1d88b60e84a6e35e2025e
Mark Abraham [Tue, 27 Sep 2011 23:47:36 +0000 (09:47 +1000)]
Added tip for converting .xpm to something useful
Originally provided by Justin Lemkul on gmx-users.
Change-Id: I92e0d17095dca5a738dbb3188067d4394742e653
Rossen Apostolov [Tue, 27 Sep 2011 00:13:59 +0000 (02:13 +0200)]
Merge "Removed CMake warning for recent OpenMPI versions" into release-4-5-patches