Carsten Kutzner [Tue, 1 Mar 2011 12:06:31 +0000 (13:06 +0100)]
Fixed bug #714: deprecated structure in gettimeofday
Justin Lemkul [Sat, 26 Feb 2011 13:32:53 +0000 (08:32 -0500)]
Another typo.
Justin Lemkul [Sat, 26 Feb 2011 13:29:23 +0000 (08:29 -0500)]
Fixed some typos in mdp_opt.html
Justin Lemkul [Fri, 25 Feb 2011 23:44:47 +0000 (18:44 -0500)]
Fixed typo in citation.
Carsten Kutzner [Fri, 25 Feb 2011 18:37:58 +0000 (19:37 +0100)]
Corrected output of a warning message.
Carsten Kutzner [Fri, 25 Feb 2011 18:30:32 +0000 (19:30 +0100)]
Added the -fix option to g_tune_pme for tuning of rcoulomb and grid
at a fixed number of PME-only nodes.
Berk Hess [Thu, 24 Feb 2011 16:39:28 +0000 (17:39 +0100)]
also renamed options to g_options in Makefile.am
Berk Hess [Thu, 24 Feb 2011 14:37:26 +0000 (15:37 +0100)]
added missing density factor to cosaccel 1/viscosity output
Berk Hess [Thu, 24 Feb 2011 13:04:14 +0000 (14:04 +0100)]
pdb model numbers now start at 1
The general pdb writing code and trjconv could write pdb files
with 0 as the first model number. The minimum been changed to 1.
This fixes #709
Szilard Pall [Wed, 23 Feb 2011 12:59:32 +0000 (13:59 +0100)]
added cmake warning when the cache generated on another host is reused
Berk Hess [Wed, 23 Feb 2011 12:51:24 +0000 (13:51 +0100)]
fixed incorrect virial and pressure averages
Removed a second, incorrect setting of flags for storage of energy averages
in mdrun.
This would cause incorrect averages of the virial and pressure to be stored
in the energy file and printed at the end of the log file when the lowest
common denominator of nstcomm, nsttcouple and/or nstpcouple was less than
nstcalcenergy. Note that the instantaneous values and the actual simulation
results were all correct.
Additionally there was a potential issue with parallel checkpoint signalling
with -gcom larger than nstlist which could lead to hanging of mdrun.
This fixes #696
Berk Hess [Mon, 21 Feb 2011 14:26:10 +0000 (15:26 +0100)]
added support for harmonic potential (bond type 7) in OpenMM
Berk Hess [Mon, 21 Feb 2011 14:24:46 +0000 (15:24 +0100)]
made maximum load balancing tunable with env.var. GMX_DLB_MAX
Berk Hess [Sun, 20 Feb 2011 18:51:10 +0000 (19:51 +0100)]
fixed dynamic load balancing inactive with -gcom and pressure scaling with -gcom when nstpcouple<nstcalcenergy
Berk Hess [Sun, 20 Feb 2011 18:49:37 +0000 (19:49 +0100)]
added some debug prints to gmxcpp.c
Sander Pronk [Sun, 20 Feb 2011 09:54:14 +0000 (10:54 +0100)]
Minor fix for when write_dhdl_file=false and delta_lambda != 0
Carsten Kutzner [Wed, 16 Feb 2011 17:05:06 +0000 (18:05 +0100)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Carsten Kutzner [Wed, 16 Feb 2011 16:37:06 +0000 (17:37 +0100)]
Fixed int overflow happening in genion when number of water molecules is large
Teemu Murtola [Wed, 16 Feb 2011 15:53:32 +0000 (17:53 +0200)]
Fixed a rare bug in selection position handling.
If the "whole" prefix was used on a position calculation that applied to
a static selection (e.g., "whole_res_com of name CA CB"), the block data
for the output positions was incorrect.
Justin Lemkul [Wed, 16 Feb 2011 15:38:39 +0000 (10:38 -0500)]
Add -tu option to g_hbond.
IssueID #580
Mark Abraham [Wed, 16 Feb 2011 06:14:00 +0000 (17:14 +1100)]
Clarified source of g_rmsf reference frame
Justin Lemkul [Tue, 15 Feb 2011 19:07:38 +0000 (14:07 -0500)]
Small fix to improve xpm2ps output
Mark Abraham [Sun, 13 Feb 2011 01:11:35 +0000 (12:11 +1100)]
Added workaround for F_GB13 duplicates
Under some conditions, identical reference bond lengths could lead to
different computed 1-3 lengths (using icc 11 and double precision, at
least). These then failed the memcmp() test that removes duplicate
parameter lists, which led to near-duplicates in the
function-parameters lists. In theory, we shouldn't test for
floating-point equality with memcmp(), but in theory the test should
work, too!
Instead of memcmp(), for F_GB13 only, tests with
gmx_within_tol(a,b,1e-6) are now used. That should be an acceptable
compromise between expected function, numerical accuracy and grompp
execution time.
IssueID #699
Mark Abraham [Sun, 13 Feb 2011 00:27:24 +0000 (11:27 +1100)]
Fixed erroneous floating-point comparison
IssueID #699
Mark Abraham [Sat, 12 Feb 2011 02:20:58 +0000 (13:20 +1100)]
Added note about doing repeat invocations of genbox
Szilard Pall [Fri, 11 Feb 2011 18:14:09 +0000 (19:14 +0100)]
fixed buggy detection of hostname and time of build in CMake
Mark Abraham [Fri, 11 Feb 2011 07:31:52 +0000 (18:31 +1100)]
Removed ancient CVS tag lines
Mark Abraham [Fri, 11 Feb 2011 07:11:18 +0000 (18:11 +1100)]
Used some spacing to make code readable
Mark Abraham [Fri, 11 Feb 2011 06:57:27 +0000 (17:57 +1100)]
Used symbolic constant more consistently
Mark Abraham [Fri, 11 Feb 2011 06:43:22 +0000 (17:43 +1100)]
Made the "multiple settles" fatal error more helpful
The error message now explains the origin of the issue, hints at a
common reason for erroneously provoking this error, and still
provides the previously-given tip for resolving the issue for users
who really need two molecule blocks of constrained solvent.
Sander Pronk [Thu, 10 Feb 2011 10:39:57 +0000 (11:39 +0100)]
Fixed a bug in g_energy -odh
Can now succesfully extract dhdl values with g_energy when
delta_lambda>0
Roland Schulz [Thu, 23 Sep 2010 05:34:02 +0000 (01:34 -0400)]
using set_mm_ps to make pgi happy
Asked about this commit 10Apr2010 and got no answer. Committing it now so that it deosn't get lost
Should have no effect on gcc and fixes it for PGI
Justin Lemkul [Thu, 3 Feb 2011 00:51:41 +0000 (19:51 -0500)]
Fixed a typo.
Mark Abraham [Wed, 2 Feb 2011 04:48:20 +0000 (15:48 +1100)]
Fixed minor issue with replica exchange
If the user chose mdrun -replex that was not a multiple of
nstcalcenergy, then replica exchange could occur when energies were
not current. Fixed by requiring repl_ex_nst to be a multiple of
nstcalcenergy, as with similar mechanisms for global
intra-simulation communication.
IssueID #695
Erik Lindahl [Sun, 30 Jan 2011 20:59:08 +0000 (21:59 +0100)]
Improved PBC handling for large molecules during cluster PBC
Erik Lindahl [Sun, 30 Jan 2011 20:15:41 +0000 (21:15 +0100)]
Fixed the pbc cluster option of trjconv by switching to a slower algorithm
David van der Spoel [Sat, 29 Jan 2011 21:19:45 +0000 (22:19 +0100)]
Merge branch 'release-4-5-patches' of git@git.gromacs.org:gromacs into release-4-5-patches
David van der Spoel [Sat, 29 Jan 2011 21:19:17 +0000 (22:19 +0100)]
Added code in g_nmeig to compute the quantum corrections to heat capacity
and enthalpy, based on a normal mode analysis.
Added one and fixed one reference in copyrite.c
Mark Abraham [Fri, 28 Jan 2011 07:38:23 +0000 (18:38 +1100)]
Added forgotten file
IssueID #690
Mark Abraham [Fri, 28 Jan 2011 07:18:38 +0000 (18:18 +1100)]
Turned g_options into a normal GROMACS tool
Made the old src/contrib/options into g_options which is built and
installed by CMake by default.
IssueID #690
Mark Abraham [Fri, 28 Jan 2011 07:02:33 +0000 (18:02 +1100)]
Renamed src/tools/options.c
IssueID #690
Mark Abraham [Fri, 28 Jan 2011 03:04:04 +0000 (14:04 +1100)]
Improved grompp documentation
Added clarification points about whether coordinates come from -t or -c
files, reworded the recommendations about restarts, and added a tip
that gmxcheck can compare .tpr files.
IssueID #688
David van der Spoel [Wed, 26 Jan 2011 19:56:23 +0000 (20:56 +0100)]
Merge branch 'release-4-5-patches' of git@git.gromacs.org:gromacs into release-4-5-patches
Mark Abraham [Tue, 25 Jan 2011 12:22:28 +0000 (23:22 +1100)]
Improved genion -h
Explicit mention is now made of the need to use the correct
molecule names for ions with -pname and -nname, and in the topology.
Mark Abraham [Tue, 25 Jan 2011 07:09:14 +0000 (18:09 +1100)]
Relocated some t_matrix documentation
Mark Abraham [Tue, 25 Jan 2011 07:06:21 +0000 (18:06 +1100)]
Improved do_dssp -ssdump output
do_dssp -sc now dumps rows of strings with the secondary structure
content for the whole trajectory. g_chi has a feature that reads in
this file, however g_chi is hard-coded to read only the first line,
so this change does not affect that feature.
IssueID #683
Mark Abraham [Tue, 25 Jan 2011 06:43:38 +0000 (17:43 +1100)]
Improved do_dssp -sc output
do_dssp -sc now computes the total for each secondary structure type.
This makes it easy to report the average secondary structure content
by type in a comment at the bottom of that file.
IssueID #683
Justin Lemkul [Mon, 24 Jan 2011 00:01:08 +0000 (19:01 -0500)]
Various small changes to the man pages.
Justin Lemkul [Sun, 23 Jan 2011 21:38:35 +0000 (16:38 -0500)]
Small fix for editconf related to formatting consistency.
IssueID #677
Mark Abraham [Sun, 23 Jan 2011 09:04:32 +0000 (20:04 +1100)]
Remove g_highway from list of programs
Mark Abraham [Sun, 23 Jan 2011 06:12:15 +0000 (17:12 +1100)]
Improved conversion of documentation to LaTeX
Sundry improvements to the way textual markup in the inline
documentation for GROMACS tools was converted into LaTeX markup via
'g_tool_name -man tex' for inclusion in the LaTeX manual.
IssueID #677
Mark Abraham [Sun, 23 Jan 2011 11:24:25 +0000 (22:24 +1100)]
Improved consistency of text style usage
All references to tool names, option names, and command line inputs
should be like '[TT]g_tool_name[tt]' or '<tt>-rerun</tt>' (depending
on the type of file), so that when it reaches the LaTeX manual, the
monospace font conveys the standard meaning, which is that this is
something the user might type.
IssueID #677
Mark Abraham [Sun, 23 Jan 2011 11:21:37 +0000 (22:21 +1100)]
Minor wording fixes
Mark Abraham [Sat, 22 Jan 2011 04:28:10 +0000 (15:28 +1100)]
Moved options.c to tools subdir
CMake doesn't work on src/contrib, so in order to get a current version
of the program options to build the manual, options.c has moved to
src/tools. Build systems have been updated accordingly. This program
will not be installed by default. CMake will build it by default, and
autotools will not.
Mark Abraham [Sun, 23 Jan 2011 00:27:48 +0000 (11:27 +1100)]
cmake: added back gsl support (GMX_GSL, disabled by default)
Conflicts:
src/tools/CMakeLists.txt
Christoph Junghans [Sat, 22 Jan 2011 18:37:45 +0000 (19:37 +0100)]
cmake: added GMX_XML to fully disable xml support
this is useful, when compiling statically and libxml2.a is missing or
libxml2 is broken for static linking
(see http://bugs.gentoo.org/show_bug.cgi?id=306479)
Christoph Junghans [Sat, 22 Jan 2011 17:46:32 +0000 (18:46 +0100)]
cmake: add support for external blas/lapack
David van der Spoel [Sat, 22 Jan 2011 09:02:58 +0000 (10:02 +0100)]
Fixed bug 678 which was due to calling gmx_fatal without calling
parse_common_args before.
Justin Lemkul [Fri, 21 Jan 2011 19:26:06 +0000 (14:26 -0500)]
Added g_pme_error to programs.txt
Justin Lemkul [Fri, 21 Jan 2011 14:55:38 +0000 (09:55 -0500)]
More minor formatting/editorial fixes for the manual.
IssueID #671
Mark Abraham [Thu, 20 Jan 2011 09:46:02 +0000 (20:46 +1100)]
Added NHE to OPLS/AA pdb2gmx hydrogen database
The pdb2gmx residue database includes the NH2 capping group, and its
synonym NHE. The latter was missing from the .hdb, which is now fixed.
Mark Abraham [Thu, 20 Jan 2011 06:10:46 +0000 (17:10 +1100)]
Made gmxdump error message clearer.
The old message was a bit cryptic about both the reason for the error,
and the suggested course of action.
Justin Lemkul [Wed, 19 Jan 2011 18:45:57 +0000 (13:45 -0500)]
Fixes to g_wham documentation.
Mostly formatting issues in the source code, making it
(hopefully) a bit easier to read and keep track of. The
help info ate up a lot of space in the manual, so the
changes I made should make it a bit more compact.
IssueID #671
Justin Lemkul [Wed, 19 Jan 2011 16:33:54 +0000 (11:33 -0500)]
Tons of tiny changes to documentation. Manual looks prettier now.
IssueID #671
Justin Lemkul [Wed, 19 Jan 2011 15:00:26 +0000 (10:00 -0500)]
Trivial fixes to program descriptions.
To keep everything in the manual consistent, a few names must
be changed to reflect the new naming scheme that has been adopted.
Justin Lemkul [Tue, 18 Jan 2011 15:21:55 +0000 (10:21 -0500)]
Fixes to the demo script.
Various typographical and editorial changes,
no major changes to functionality.
IssueID #669
Mark Abraham [Tue, 18 Jan 2011 01:36:43 +0000 (12:36 +1100)]
Improved .mdp file comment about the 'define' field
The -D examples were less helpful than the new ones, which provide
a hint not to use -DPOSRE, and a clue that variable names are
case-sensitive.
Justin Lemkul [Mon, 17 Jan 2011 22:16:12 +0000 (17:16 -0500)]
Fixes to methanol and mixed demos. Issue ID #669
Justin Lemkul [Mon, 17 Jan 2011 20:42:44 +0000 (15:42 -0500)]
Removed non-existent program and redundant information to clean up manual
Berk Hess [Mon, 17 Jan 2011 17:21:19 +0000 (18:21 +0100)]
fixed incorrect parameter declarations in gmx_fft_fftw2.c
Justin Lemkul [Mon, 17 Jan 2011 12:50:04 +0000 (07:50 -0500)]
Various editorial and formatting fixes
Mark Abraham [Mon, 17 Jan 2011 09:19:20 +0000 (20:19 +1100)]
Fix Angstrom <=> nm error in documentation
The default value for gb_dielectric_offset .mdp parameter was
listed as 0.09 nm. In the code it is 0.009 nm, which is what it
should be, per the original literature.
Justin Lemkul [Fri, 14 Jan 2011 14:00:18 +0000 (09:00 -0500)]
Fixes to grompp -maxwarn documentation. Issue ID #627
Mark Abraham [Thu, 13 Jan 2011 08:37:58 +0000 (19:37 +1100)]
Made src/kernel/repl_ex.c legible
Some of the formatting was extremely awkward to read, so I
re-formatted the whole file with emacs using the formatting line, and
added braces where consistent with the coding conventions.
IssueID #664 point 2.
Berk Hess [Mon, 10 Jan 2011 09:12:12 +0000 (10:12 +0100)]
fixed zero viscosity energy/log file output with cos_acceleration
Mark Abraham [Fri, 7 Jan 2011 23:12:03 +0000 (10:12 +1100)]
Added note that g_msd -mol does treat PBC (by making molecules whole)
Mark Abraham [Fri, 7 Jan 2011 22:55:00 +0000 (09:55 +1100)]
Implemented effective test for MPI_IN_PLACE, thanks to Michael Wild on the CMake mailing list. Fixes #594
Mark Abraham [Thu, 6 Jan 2011 09:19:56 +0000 (20:19 +1100)]
Stop CMake defaulting to turning off compiler warnings for Intel
compilers, since a) warnings are useful, and b) we show all warnings
with GCC.
ckutzne [Tue, 4 Jan 2011 17:28:12 +0000 (18:28 +0100)]
Fixed inconvenient output file names if -sep is used in combination with -nzero.
For the first file (numbered 0) there was one digit too many,
now all file numbers have nzero digits.
Berk Hess [Tue, 4 Jan 2011 15:18:20 +0000 (16:18 +0100)]
fixed grompp looking for include files in double relative paths, for instance in ../.. with ../topol.top
David van der Spoel [Sun, 26 Dec 2010 18:08:13 +0000 (19:08 +0100)]
Merge branch 'release-4-5-patches' of git@git.gromacs.org:gromacs into release-4-5-patches
David van der Spoel [Sat, 25 Dec 2010 08:55:12 +0000 (09:55 +0100)]
Added warning in g_dipoles
Removed heat capacity calculation from g_energy.
David van der Spoel [Thu, 23 Dec 2010 08:19:48 +0000 (09:19 +0100)]
Fixed bug in statistics which did not allow fitting with weights.
Added check for return value from statistics codes in g_analyze.
Berk Hess [Wed, 22 Dec 2010 09:44:17 +0000 (10:44 +0100)]
removed incorrect citation print of Engin2010 for pull groups of a single atom
Berk Hess [Tue, 21 Dec 2010 14:38:44 +0000 (15:38 +0100)]
pme.c work-around for MPI fatal error in pme with partticle decomposition
Berk Hess [Thu, 16 Dec 2010 20:28:44 +0000 (21:28 +0100)]
fixed incorrect LJ table in mdrun with reppow!=12
Berk Hess [Thu, 16 Dec 2010 10:41:15 +0000 (11:41 +0100)]
removed editconf warning on box distance with -bt
Berk Hess [Mon, 13 Dec 2010 16:45:35 +0000 (17:45 +0100)]
fixed tpbconv time options leading to negative nsteps for nsteps larger than INT_MAX
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 20:34:05 +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 11:26:42 +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.
ckutzne [Thu, 2 Dec 2010 14:44:41 +0000 (15:44 +0100)]
Fixed typo.
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 10:11:57 +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.
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