Rossen Apostolov [Fri, 9 Sep 2011 14:28:50 +0000 (16:28 +0200)]
Added support for custom external BLAS/LAPACK libraries.
To use them give give to cmake
-DGMX_EXTERNAL_LAPACK=TRUE and
-DGMX_LAPACK_USER=/path/to/external/lapack
Same for BLAS.
Change-Id: I4ca1c4ca365788fcafc4219934fdfe8758db84f1
Mark Abraham [Tue, 6 Sep 2011 01:44:43 +0000 (11:44 +1000)]
Fix bug with large ints without MPI_IN_PLACE
Communication of gmx_large_int_t arrays when MPI_IN_PLACE was disabled
never worked when it was introduced just before 4.5.4, because it used
an int-sized buffer. This affected replica exchange sanity tests on the
number of steps.
IssueID #801 #803
Change-Id: I48f04b1c4dd80646711db99c5dab89cb910e79b4
Michael Shirts [Mon, 5 Sep 2011 14:32:12 +0000 (16:32 +0200)]
Merge "fixed incorrect pV term in the energy file" into release-4-5-patches
Mark Abraham [Thu, 1 Sep 2011 14:25:31 +0000 (00:25 +1000)]
Made grompp note about non-zero charge more useful
Non-programmers need not know what -6.
300000e-1 actually means,
so we should avoid the %e printf format. URL provided to discussion
of why the user needs to pay some attention here.
Change-Id: Ie593919540db8728b898cd7d0904659c7f3d9345
Mark Abraham [Thu, 25 Aug 2011 04:58:38 +0000 (14:58 +1000)]
Re-implemented generating default protein index groups
Hopefully using a struct to associate data that is used in association
will make future maintenance easier. Some general improvements
to the code quality, also.
Change-Id: I37017e1dd3612d143df935ada79374dd9a8fbcd3
Mark Abraham [Thu, 25 Aug 2011 02:01:17 +0000 (12:01 +1000)]
Adjusted construction of default index groups
The CHARMM convention of naming the H atom bonded to backbone N as
"HN" led to erroneous construction the MainChain+H and (complementary)
SideChain groups. Protein, Protein-H and SideChain-H were fortuitously
correct.
IssueID #788
Change-Id: Ib8525dba61e4f072ae5074a9f6b523ac13892833
Mark Abraham [Thu, 25 Aug 2011 02:00:45 +0000 (12:00 +1000)]
Fixed comment
Change-Id: I42e6292e7c658c69810626cf4e6c861394546a40
Berk Hess [Mon, 29 Aug 2011 13:24:10 +0000 (15:24 +0200)]
fixed incorrect pV term in the energy file
Change-Id: I157b0468907802e29c7dec763ed2e5db99c02922
Carsten Kutzner [Wed, 24 Aug 2011 15:20:38 +0000 (17:20 +0200)]
Instead of a segv, mdrun now gives an error msg if npme>np, fixes #795
Instead of a segv, mdrun now gives an error msg if npme>np, fixes #795
Change-Id: I2e93bccf45ace215d6237354559b8750628a13d6
Roland Schulz [Tue, 23 Aug 2011 07:22:17 +0000 (09:22 +0200)]
Merge "Fixed g_disre dereferencing cr" into release-4-5-patches
Roland Schulz [Tue, 23 Aug 2011 07:21:34 +0000 (09:21 +0200)]
Merge "Typo fix" into release-4-5-patches
Roland Schulz [Tue, 23 Aug 2011 07:21:00 +0000 (09:21 +0200)]
Merge "fixed operation on closed file structure in gmx_rmsdist, fixes #780" into release-4-5-patches
Roland Schulz [Tue, 23 Aug 2011 07:19:31 +0000 (09:19 +0200)]
Merge "fixed possible infinite loop when reading atom types, fixes #791" into release-4-5-patches
Mark Abraham [Tue, 23 Aug 2011 05:58:13 +0000 (15:58 +1000)]
Fixed g_disre dereferencing cr
mdrun uses some code in common with g_disre, and some code that deals
with PD vs DD has to use cr. g_disre sets cr to NULL, of course, and
the common code just needs to be sensitive to that and test for NULL
before using it.
IssueID #766
Change-Id: Ia92bd1d18ba8085d285f37b14897f384a71c64ce
Mark Abraham [Tue, 23 Aug 2011 05:58:04 +0000 (15:58 +1000)]
Typo fix
Change-Id: I0fd1e3f6e21c3fedcb43151935bbfc7fe69d84bd
Berk Hess [Mon, 22 Aug 2011 15:20:34 +0000 (17:20 +0200)]
fixed operation on closed file structure in gmx_rmsdist, fixes #780
Change-Id: Iddac26debf616d962df2fd40b79d01dc01942c1c
Berk Hess [Mon, 22 Aug 2011 14:33:36 +0000 (16:33 +0200)]
fixed possible infinite loop when reading atom types, fixes #791
Change-Id: If5ddcc0b5238cdfa625b1d85d05e1dabbe4eb32a
Mark Abraham [Fri, 19 Aug 2011 15:59:09 +0000 (01:59 +1000)]
Explained terminal residues and AMBER in pdb2gmx -h
The -ter mechanism doesn't work because naming terminal residues with
suitable prefixes is required.
Change-Id: Idde88d84988ef4d1d0752e6f854a0d18c194ea88
Mark Abraham [Tue, 16 Aug 2011 11:37:00 +0000 (21:37 +1000)]
Made free energy perturbation work with CMAP
That is, FEP of other parameters works when CMAP is active, not
FEP of CMAP parameters themselves (if that even makes sense!)
Berk Hess [Mon, 15 Aug 2011 10:00:45 +0000 (12:00 +0200)]
fixed incorrect pointer assignment in g_protonate
Change-Id: I719c24921157077aca60afae1e4579b7dcf670e3
Berk Hess [Fri, 12 Aug 2011 08:16:37 +0000 (10:16 +0200)]
implemented full exclusion support for the charge-group innerloops
Change-Id: Ib662addaf9e33288c072ee05446d883bac09394c
Roland Schulz [Thu, 11 Aug 2011 17:25:55 +0000 (19:25 +0200)]
Merge "removed npmenodes mismatch warning in read_checkpoint without DD" into release-4-5-patches
Berk Hess [Thu, 11 Aug 2011 13:44:54 +0000 (15:44 +0200)]
Merge "Make sure that ftell works correctly for files opened in append mode fixing Issue #762" into release-4-5-patches
Roland Schulz [Tue, 26 Jul 2011 07:24:33 +0000 (03:24 -0400)]
Make sure that ftell works correctly for files opened in append mode
fixing Issue #762
Change-Id: I019fa6a2b51a2156c900e1a31a0b521e62b79961
Berk Hess [Wed, 10 Aug 2011 07:52:15 +0000 (09:52 +0200)]
removed npmenodes mismatch warning in read_checkpoint without DD
Berk Hess [Wed, 10 Aug 2011 07:50:39 +0000 (09:50 +0200)]
removed fatal_error for prime number of nodes when -npme is set
Mark Abraham [Tue, 2 Aug 2011 23:08:01 +0000 (09:08 +1000)]
Fixed output bug in demux.pl
Simulation time written to the output index files was limited to
8 characters, which was too small. Now 20 characters.
Carsten Kutzner [Tue, 2 Aug 2011 13:10:41 +0000 (15:10 +0200)]
Typo.
Berk Hess [Tue, 2 Aug 2011 10:24:44 +0000 (12:24 +0200)]
made trjconv -novel work again, fixes #722
Carsten Kutzner [Fri, 29 Jul 2011 08:41:25 +0000 (10:41 +0200)]
Fixed calculation of max and min number of PME-only nodes. Fixes #787.
Michael Shirts [Fri, 22 Jul 2011 04:41:14 +0000 (00:41 -0400)]
number of degrees of freedom can be fractional -- in NHC_trotter, 'nd' has to be double, not int.
Justin A. Lemkul [Wed, 20 Jul 2011 16:50:05 +0000 (12:50 -0400)]
Removed jargon and abbreviations from pdb2gmx.
Not everyone will know what 'iso' means. These little tweaks
will hopefully lead to better understanding of the pdb2gmx options.
David van der Spoel [Wed, 20 Jul 2011 09:24:05 +0000 (11:24 +0200)]
Merge branch 'release-4-5-patches' of git@git.gromacs.org:gromacs into release-4-5-patches
David van der Spoel [Wed, 20 Jul 2011 09:21:30 +0000 (11:21 +0200)]
Added initialization of arrays after srenew call.
Mark Abraham [Sun, 17 Jul 2011 22:06:13 +0000 (08:06 +1000)]
Streamlined small part of pdb2gmx
In the absence of manual assignment of histidine protonation, the
automated assignment mechanism analysed the existence of hydrogen
bonds before determining whether any histidine residues existed in
the current chain. This led to confusing output on (for example)
DNA chains.
This improvement checks for the existence of at least one histidine
before analysing and reporting on the hydrogen-bonding network.
Thus pdb2gmx will process chains lacking histidine slightly faster,
and be negligibly slower for those including a histidine.
It's also a little more verbose about why it is searching for
hydrogen-bonding networks.
Mark Abraham [Fri, 15 Jul 2011 12:14:43 +0000 (22:14 +1000)]
Reading a .g96 trajectory now causes fatal error
When someone fixes the .g96 reading code to be thread-safe and
correct, this functionality can be re-instated.
IssueID #781
Berk Hess [Wed, 13 Jul 2011 15:48:06 +0000 (17:48 +0200)]
fixed div by 0 in compute_io, fixes #778
Carsten Kutzner [Mon, 11 Jul 2011 11:02:39 +0000 (13:02 +0200)]
Added two missing headers
Mark Abraham [Mon, 11 Jul 2011 07:31:31 +0000 (17:31 +1000)]
Fix some identifier naming issues in last commit
That'll teach me not to avoid doing a test compilation! :-(
Mark Abraham [Mon, 11 Jul 2011 07:00:47 +0000 (17:00 +1000)]
Avoided some integer overflows
With very large numbers of PME nodes and/or Fourier grid points,
integer overflows could occur in comm_cost_est(). Now fixed.
Mark Abraham [Sat, 2 Jul 2011 01:15:47 +0000 (11:15 +1000)]
Clarified use of OPLS/AA zwitterion termini
These are only for use with single-residue amino acids
Mark Abraham [Tue, 5 Jul 2011 06:24:34 +0000 (16:24 +1000)]
Fixed improper file close with GB and mdrun -debug
Mark Abraham [Sat, 2 Jul 2011 01:15:21 +0000 (11:15 +1000)]
Made pdb2gmx error message less cryptic
Carsten Kutzner [Wed, 6 Jul 2011 07:43:33 +0000 (09:43 +0200)]
Added globsig.h to include/types/Makefile.am
David van der Spoel [Fri, 1 Jul 2011 21:14:37 +0000 (23:14 +0200)]
Merge branch 'release-4-5-patches' of git@git.gromacs.org:gromacs into release-4-5-patches
Christoph Junghans [Fri, 1 Jul 2011 11:51:29 +0000 (13:51 +0200)]
dl lib was missing in libgmx.pc if GMX_DLOPEN is enabled
Justin A. Lemkul [Fri, 1 Jul 2011 00:45:10 +0000 (20:45 -0400)]
Fixed PME citation.
IssueID #769
Justin A. Lemkul [Wed, 29 Jun 2011 19:32:38 +0000 (15:32 -0400)]
Fixes for g_bar output. Units are now correct.
Mark Abraham [Wed, 29 Jun 2011 03:08:57 +0000 (13:08 +1000)]
Revert "draft"
This reverts commit
89abdeb7fa078c7b8dd4391aad3df2c03a60a2f0.
Oops, stuff from the gmx_packed_t branch leaked in. Sorry.
Mark Abraham [Wed, 29 Jun 2011 01:14:05 +0000 (11:14 +1000)]
Improved error message and documentation
-pbc mol now notes the need for a -s .tpr file. Also, when the index
groups (perhaps implicitly defined by a .tpr file) do not match the
input trajectory, the error message now hints that a mismatch exists.
For example, this wil help users trying to visualize the results of
genion by way of "trjconv -pbc mol -ur compact", by erroneously
using the .tpr file that was input to genion in combination with its
output file.
Mark Abraham [Sun, 19 Jun 2011 13:21:03 +0000 (23:21 +1000)]
draft
Berk Hess [Thu, 23 Jun 2011 10:58:12 +0000 (12:58 +0200)]
tpbconv can now read cpt files, fixes #741
Berk Hess [Wed, 22 Jun 2011 14:49:16 +0000 (16:49 +0200)]
fixed convergence of multiple pull constraints
With multiple constraint pull groups, only the convergence
of the last group was checked. This fixes #657
Justin A. Lemkul [Tue, 21 Jun 2011 16:40:23 +0000 (12:40 -0400)]
Fixed typos.
Justin A. Lemkul [Tue, 21 Jun 2011 14:36:33 +0000 (10:36 -0400)]
Made grompp fatal error a little more explicit.
Mark Abraham [Mon, 23 May 2011 01:14:37 +0000 (11:14 +1000)]
Expanded LINCS warning text
It now indicates which simulation in a multi-sim is the culprit
Sander Pronk [Mon, 20 Jun 2011 09:26:09 +0000 (11:26 +0200)]
Fixed symtab buffer error message.
Symtab error message now a little less cryptic. Buffer size increased to 1024.
Christoph Junghans [Thu, 16 Jun 2011 07:29:24 +0000 (09:29 +0200)]
cmake: rename LIB to GMXLIB to avoid conflict with FindMPI.cmake
IssueID #763
Berk Hess [Fri, 10 Jun 2011 16:52:50 +0000 (18:52 +0200)]
fixed grompp enx Nose-Hoover Xi reading, fixes #759
David van der Spoel [Fri, 10 Jun 2011 06:26:11 +0000 (08:26 +0200)]
Merge branch 'release-4-5-patches' of git@git.gromacs.org:gromacs into release-4-5-patches
Justin A. Lemkul [Thu, 9 Jun 2011 21:39:52 +0000 (17:39 -0400)]
genion and genbox now print in a consistent manner.
Christoph Junghans [Thu, 9 Jun 2011 11:57:16 +0000 (13:57 +0200)]
Merge branch 'release-4-5-patches' of git://git.gromacs.org/gromacs into release-4-5-patches
Christoph Junghans [Thu, 9 Jun 2011 09:42:30 +0000 (11:42 +0200)]
Added a comment where bPhobics comes from
IssueID #754
Berk Hess [Thu, 9 Jun 2011 07:14:36 +0000 (09:14 +0200)]
fixed dirrent_t memory allocation issue on Solaris, fixes #739
Christoph Junghans [Wed, 8 Jun 2011 14:27:03 +0000 (16:27 +0200)]
removed duplicated bPhobics function (thx to Francois Bissey)
IssueID #754
Christoph Junghans [Wed, 8 Jun 2011 14:07:56 +0000 (16:07 +0200)]
cmake: remove selection/test* from gmxlib sources
IssueID #749
Sander Pronk [Wed, 8 Jun 2011 13:57:34 +0000 (15:57 +0200)]
Added support for SunCC on Solaris/SPARC.
Based on a patch provided by Sergey Klyaus.
Sander Pronk [Wed, 8 Jun 2011 12:09:46 +0000 (14:09 +0200)]
Adressed over-eager warnings that gcc 4.5 generates.
Justin A. Lemkul [Wed, 8 Jun 2011 00:55:21 +0000 (20:55 -0400)]
Minor clarifications to g_rotacf help information.
Mark Abraham [Tue, 7 Jun 2011 05:45:25 +0000 (15:45 +1000)]
Fixed spelling of reproducible
Yes, English is stupid.
David van der Spoel [Tue, 31 May 2011 07:18:46 +0000 (09:18 +0200)]
Further patches to fluctuation code and density of states code.
David van der Spoel [Tue, 31 May 2011 07:18:02 +0000 (09:18 +0200)]
Added quote.
David van der Spoel [Tue, 31 May 2011 07:16:31 +0000 (09:16 +0200)]
Merge branch 'release-4-5-patches' of git@git.gromacs.org:gromacs into release-4-5-patches
Carsten Kutzner [Mon, 30 May 2011 09:36:02 +0000 (11:36 +0200)]
Flooding as harm. restraint: Abort when origin position is ambiguously set in edi file. Thanks to B. Voss for reporting this.
Justin A. Lemkul [Thu, 26 May 2011 15:52:22 +0000 (11:52 -0400)]
Fixes to sugar dihedrals.
The force field files distributed by GROMOS (i.e., via ATB) were
incorrect. The GROMACS files matched these files exactly, thus
propagating the incorrect parameters. The sugar dihedrals now match
the most recent version of the 53A5 and 53A6 force field files
distributed via ATB.
IssueID #668
David van der Spoel [Mon, 23 May 2011 20:13:23 +0000 (22:13 +0200)]
Merge branch 'release-4-5-patches' of git@git.gromacs.org:gromacs into release-4-5-patches
David van der Spoel [Mon, 23 May 2011 20:11:15 +0000 (22:11 +0200)]
Re-implemented the fluctuation analysis, based on Enthalpy, Volume,
Temperature and/or Total Energy. Now correct as well.
Rossen Apostolov [Wed, 18 May 2011 13:47:31 +0000 (15:47 +0200)]
Fixed g_tcaf citation in html docs
Berk Hess [Tue, 17 May 2011 10:06:50 +0000 (12:06 +0200)]
fixed minor memory leak with particle decomposition, fixes #752
Roland Schulz [Sun, 15 May 2011 09:48:26 +0000 (05:48 -0400)]
corrected typo: if(errno=EINVAL)
Berk Hess [Thu, 12 May 2011 15:07:52 +0000 (17:07 +0200)]
removed memory allocation/free during constraining
Mark Abraham [Wed, 11 May 2011 23:30:47 +0000 (09:30 +1000)]
Added reference to g_sas -h
Reference provided by Xavier Periole on gmx-users
Mark Abraham [Wed, 11 May 2011 23:30:25 +0000 (09:30 +1000)]
Cleaned up g_sas help text
Justin A. Lemkul [Wed, 11 May 2011 13:15:13 +0000 (09:15 -0400)]
Fixed typo.
Justin A. Lemkul [Tue, 10 May 2011 20:45:06 +0000 (16:45 -0400)]
Fixed g_dipoles help description. Fixed spacing and removed non-existent
command line argument.
Erik Marklund [Tue, 10 May 2011 12:37:55 +0000 (14:37 +0200)]
Merge branch 'release-4-5-patches' of git@git.gromacs.org:gromacs into release-4-5-patches
Erik Marklund [Tue, 10 May 2011 12:37:48 +0000 (14:37 +0200)]
Increased debugging output
Erik Marklund [Tue, 10 May 2011 12:37:10 +0000 (14:37 +0200)]
Fixed long standing bug where the merging resulted in too few hbonds.
Mark Abraham [Mon, 9 May 2011 05:30:48 +0000 (15:30 +1000)]
Added hint about calling trjconv more than once
Mark Abraham [Mon, 9 May 2011 05:30:20 +0000 (15:30 +1000)]
Spaced out paragraphs in trjconv help
David van der Spoel [Sat, 7 May 2011 19:27:39 +0000 (21:27 +0200)]
Added computation of A and U.
David van der Spoel [Fri, 6 May 2011 13:06:17 +0000 (15:06 +0200)]
Updated, made default tolerance for bisector more stringent and used double
all the way for computing fluidicity.
David van der Spoel [Fri, 6 May 2011 12:01:24 +0000 (14:01 +0200)]
Fixed weight functions and added -dump option (hidden) to make graphs for
debugging.
David van der Spoel [Fri, 6 May 2011 06:45:44 +0000 (08:45 +0200)]
Updated. Fixed computation of frequency.
David van der Spoel [Fri, 6 May 2011 06:44:09 +0000 (08:44 +0200)]
Merge branch 'release-4-5-patches' of git@git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Thu, 5 May 2011 10:58:37 +0000 (11:58 +0100)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Thu, 5 May 2011 10:58:28 +0000 (11:58 +0100)]
Update doc to clarify that Amber nucleic params are from Amber94 (recommendation by Adrian Rothberg)
David van der Spoel [Mon, 2 May 2011 18:41:35 +0000 (20:41 +0200)]
Updated the eqn for computing Delta. Now get roughly the right f.
Mark Abraham [Mon, 2 May 2011 13:09:10 +0000 (23:09 +1000)]
Removed duplicate definition of md_print_warning()
IssueID #738
Erik Marklund [Mon, 2 May 2011 12:19:46 +0000 (14:19 +0200)]
Commented out re-declaration of md_print_warning()