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2012-10-03Bump all packages that use perl, or depend on a p5-* package, orwiz5-9/+10
are called p5-*. I hope that's all of them.
2012-10-02Mass recursive bump after the dependence fix of the "cairo" packagetron3-6/+6
requested by Thomas Klausner.
2012-09-16CONFLICTS with generate-[0-9]*; ++pkgrevisioncheusov1-1/+4
2012-09-15recursive bump from libffi shlib major bumpobache3-6/+6
(additionaly, reset PKGREVISION of qt4-* sub packages from base qt4 update)
2012-09-14Fix PKGNAME.asau1-1/+2
2012-09-14+ plinkasau1-1/+2
2012-09-14Remove errorneously imported backup file. (Why was it not ignored??)asau1-1/+0
2012-09-14Import PLINK 1.07 as biology/plinkasau6-0/+134
From Jason Bacon via pkgsrc-wip. PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.
2012-09-11"user-destdir" is default these daysasau31-88/+31
2012-09-07Revbump after updating graphics/cairoadam3-5/+6
2012-08-30more omf-scrollkeeper missingdrochner1-1/+2
2012-08-16Update to 0.12.13ryoon2-6/+6
Changelog: Version 0.12.13 GChemPaint: * Fix View::BuildSVG() and View::BuildEPS() which were missing the trailing 0. * Fix loading of arrows inside a group. [#27032]
2012-07-03Update to 0.12.12ryoon3-9/+9
Changelog: Version 0.12.12 GCrystal: * Fix atoms loading. * Fix infinite loop condition. [#36583] Version 0.12.11 GChemPaint: * fixed text position serialization. [#34947] * fixed crash when selecting the alignment item inside a mechanism step. [#35626]
2012-06-14Recursive PKGREVISION bump for libxml2 buildlink addition.sbd5-7/+10
2012-04-08All supported python versions in pkgsrc support eggs, so removewiz1-2/+2
${PLIST.eggfile} from PLISTs and support code from lang/python.
2012-04-08Remove python24 and all traces of it from pkgsrc.wiz1-3/+1
Remove devel/py-ctypes (only needed by and supporting python24). Remove PYTHON_VERSIONS_ACCEPTED and PYTHON_VERSIONS_INCOMPATIBLE lines that just mirror defaults now. Miscellaneous cleanup while editing all these files.
2012-03-03More pcre PKGREVISION bumps.wiz1-2/+2
2012-03-03Recursive bump for pcre-8.30* (shlib major change)wiz2-4/+4
2012-02-07Add csh scripts to REPLACE_CSH and add USE_TOOLS+=csh:runsbd1-2/+5
Bump PKGREVISION
2012-02-06Revbump forwiz3-4/+6
a) tiff update to 4.0 (shlib major change) b) glib2 update 2.30.2 (adds libffi dependency to buildlink3.mk) Enjoy.
2012-01-14Update to Gromacs 4.5.5asau3-8/+25
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.
2012-01-08Update to 1.6.13.ryoon2-8/+7
Changelog: Fixes and enhancements in chemtool 1.6.13 - New export option "ASY" for Asymptote files (http://asymptote.sourceforge.net) - Added support for Unicode symbol characters inserted e.g. by cut-and-paste from LibreOffice - Fixed build with newer linkers that do not resolve indirect requirements automatically - Rewritten logic for choosing to include national language support during build - Fixed crash on startup due to errors in menu icon setup - Batch mode could crash due to incomplete initialisation of color arrays - Undo/redo in "move fragment"-mode did not work as intended - Default extension is now appended to the save filename as needed - Fixed exporting to files or directories containing spaces in their names
2011-12-09PKGREV bump for libXp-less openmotifdrochner1-2/+2
2011-11-25Remove concurrently created patch.joerg2-14/+1
2011-11-24Fix build with GCC 4.5joerg2-1/+14
2011-11-23biology/mummer: Put sort function in scopemarino2-1/+14
Add <algorithm> header for sort, DragonFly's compiler needs it. No PKGREVISION bump required.
2011-11-22Update to 0.12.10ryoon2-7/+6
Changelog: Version 0.12.10 GCrystal: * show only atoms from the first crystal when loading a CIF file with several structures. * don't crash when loading a file with invalid atoms. * don't display two atoms at the same position. * don't loose the radius ratio on serialization. Other: * fix build with most recent glib-2.0 and xulrunner. * enhanced translation: de.
2011-11-01Recursive bump for graphics/freetype2 buildlink addition.sbd1-1/+2
2011-11-01Recursive bump for graphics/freetype2 buildlink addition.sbd2-2/+4
2011-10-31Initial import of primer3.brook6-1/+96
Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.
2011-10-28python24 is not acceptable.obache1-1/+3
2011-10-27Update py-mol to 1.4.1.obache3-39/+238
many improvements and bug fixes.
2011-10-07Fix impossible depends.dholland1-2/+2
2011-10-05Add bodr, chemical-mime-data, gnome-chemistry-utils, and openbabel.ryoon1-1/+5
2011-10-05Reset MAINTAINER, because no response.ryoon2-4/+4
2011-10-05Initial import of gnome-chemistry-utils-0.12.9 from wip/gnome-chemistry-utilsryoon4-0/+365
GChemPaint, a 2D chemical editor and some other programs related to chemistry suitable for the GNOME desktop. The Gnome Chemistry Utils include three utilities: - a 2D chemical editor (GChemPaint). - a chemical calculator (computes raw formule, molar weight, mass composition, etc..) and isotopic pattern). - a molecule 3d viewer using OpenGL to display molecular models. - a crystal structues viewer and editor. - a periodic table of the elements. - a spectrum viewer. These programs are based on an included C++ library which provides a few widgets and various classes, some related to chemistry and some utility classes.
2011-10-05Initial import of openbabel-2.3.0 from wip/openbabelryoon7-0/+338
Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
2011-10-05Import of chemical-mime-data-0.1.94 as biology/chemical-mime-dataryoon5-0/+115
from wip/chemical-mime-data The chemical-mime-data package is a collection of data files to add support for various chemical MIME types on Linux/UNIX desktops, such as KDE and GNOME. Chemical MIMEs were proposed in 1995, though it seems they have never been registered with IANA. But they are widely used and the project's aim is, to support these important, but unofficial MIME types.
2011-10-05Initial import of bodr-9 from wip/bodrryoon5-0/+60
The Blue Obelisk Data Repository lists many important chemoinformatics data such as element and isotope properties, atomic radii, etc. including references to original literature. Developers can use this repository to make their software interoperable.
2011-08-14Revision bump after updating perl5 to 5.14.1.obache1-2/+2
2011-04-22recursive bump from gettext-lib shlib bump.obache2-3/+4
2011-03-23Update to Gromacs 4.5.4:asau3-7/+8
* Fixed pdb2gmx picking up force field from local instead of library directory * Made pdb2gmx vsite generation work again for certain His namings. * Fixed incorrect virial and pressure averages with certain nst... values (instantaneous values correct) * Fixed incorrect cosine viscosity output * New -multidir alternative for mdrun -multi option * Several minor fixes in analysis tools * Several updates to the program documentation
2011-01-13png shlib name changed for png>=1.5.0, so bump PKGREVISIONs.wiz1-2/+2
2010-12-30Remove RCS directory, or may failed to patch due to locked under RCS.obache1-1/+4
2010-11-23Update to Gromacs 4.5.3asau3-14/+18
This is maintainance release, it fixes: * Double precision energy file reading * CHARMM and GB issues * Support for Altivec (PowerPC) with CMake * Running binaries within the CMake build tree is now possible * Various other issues
2010-10-21GROMACS team released another version a day after:asau3-7/+14
4.5.1-20100902-2d7e855 vs. 4.5.1-20100903-d982058 call it 4.5.1.1 This looks like bug fix, changes mostly affect NT, AIX, and HP-UX.
2010-09-19Update puzzle to 5.2.obache3-17/+20
Based on PR#43775 by Kamel Derouiche. 5.2 14.07.2004 - Version 5.2 !!! NEW RELEASE =========== 5.2.rc17 14.07.2004 - Manual sources moved out of the package - numerous changes in the manual 5.2.rc16 12.07.2004 - Makefile.am: double distclean rule removed - fflush added before mygets() - because of Windows - manual spell-checked - '-consmrel' fixed - usage message extended 5.2.rc15 09.07.2004 - many changes to the manual 5.2.rc14 01.07.2004 - test suite checked, notice about results added 5.2.rc13 01.07.2004 - a number of small fixes (alloc and dealloc in epe) - convergence output for user branches fixed - G-T rate output precision fixed - tests checked and fixed 5.2.rc12 30.06.2004 - branch length convergence output corrected for user set branch lengths (i.e. no estimate) - avergedist updated: output of min/max/var/std.dev. - tstvratio and yrtsratio - no output for GTR - some future cmdline flags added to help - -prefix, -sub50, -randseed moved to usage output - -randseed=# added - release date changed in code 5.2.rc11 18.06.2004 - flags to set epsilon values added for debugging (dependent on USE_ADJUSTABLE_EPS compiler switch) 19.06.2004 - quartet percent computation fixed: quartet sums moved qinfomatr[0] -> qinfomatr[8] qinfomatr[0]=missing qs. (release 5.2.rc9) - character state output added to R/Q matrix output - average computation of dist-matrix changed: mean=average, variance, std deviation TODO: proper output / use Korbis S.E. method 25.06.2004 - GTR model ready, menu order HKY, TN, GTR, (SH), HKY 29.06.2004 - many changes to the manual 5.2.rc10 11.06.2004 - fixed no quartets in parameter estimtion for <4 seqs 15.06.2004 - computation of Bayesian weights moved into subroutine loglkl2weight. - use subroutine loglkl2weight in parallel code -> fixing division by zero bug 5.2.rc9 11.06.2004 - sequence number check for <4 and >257 added <4 - no quartet methods available >257 - no quartet puzzling available - counting for missing quartets added for parallel message checking (TODO: handling and checking) - output of root branch name added for clock analysis (sequence name or "internal branch") 5.2.rc8 04.05.2004 - tree tests move to treetest.c/treetest.h - comments added - typo corrected (suset -> subset) 08.06.2004 - ELW: continue counting p, when significantly worse - 1sKH/2sKH: restrict tests to 3 digits (0.00) (test behaviour: seems not to use some trees (KH), see above - used, but too low variance) 5.2.rc7 12.02.2004 - corrected typos in usage/README 20.02.2004 - cmdline: prefix flag fixed 22.02.2004 - '-wsr/-wsl' flags fixed: output file and file name output 5.2.rc6 25.11.2003 - 'FPRINTF...' changed to 'fprintf(STDOUT,' - strcpy added in openfile-routines 5.2.rc5 25.11.2003 - filename length chack added - typo FILENAMELENTH corrected 5.2.rc4 19.11.2003 - minor corrections: int/uli comparisons - SPRNG added to src/sprng - src/sprng autoconf/automake setup - Parallel Parameter Estimation (JPDC, Ekki 1) 5.2.rc3 07.11.2003 - WAG Matrix code/docu corrected (Goldman) TODO: remove additional output for printrmat TODO: make PEPS* smaller to have better accuracy in parameter estimation. 5.2.rc2 01.09.2003 - bug from 5.1.pl29 found and eliminated alloc size wrong: worked if Maxsubset<=Maxspc TODO: remove out-commented debug messages 5.2.rc1 20.08.2003 - first release candidate for tree-puzzle 5.2 CODE FREEZE =========== 5.1.pl30 20.08.2003 - naming convention changed for manual name input to use FILENAME.puzzle, ... 5.1.pl29 23.07.2003 - new compiler warnings fixed - index error naming fixed - debugging of matrix based permutation (not finished) 5.1.pl28 01.07.2003 - cmdline flags to switch off ml branch lengths (-notreelh), tree tests (-notreetest) 5.1.pl27 24.06.2003 - output quartet support for incorporated split in report file 5.1.pl26 06.06.2003 - menu order of tree reconstruction methods altered to QP, user tree, consensus, dist (no tree) (last two switched) 5.1.pl25 05.06.2003 - small changes to fix compiler warnings 5.1.pl24 04.06.2003 - changes from benchmark-branch merged: debug output removed - checktime fixed: sumtodo <-> done for quartets 5.1.pl23 26.05.2003 - puzzle.c: CONSENSUS -> QUARTPUZ, allocated unnecessary memory - additional malloc-checks added (if buffer == NULL) 01.06.2003 - mlmode conditions with readable constants (ml2.c,ml.h) - garbage collection in tree2bipart/subtree2bipart 5.1.pl22 16.05.2003 - fixing Array Bound Read in fputid (bug had no effect, but was read before check) - garbage collection completed in p-step algorithms and node-label (free_tree/internalnode), trueIDtmp (allpstep), - small fix in test script and rebuild of check-files 5.1.pl21 14.05.2003 - fixing free of all allocations in puzzling step (mrca, recur, split, orig) 5.1.pl20 05.05.2003 - small fix in recursive Alg. (recur.c) - debug output removed - cross check removed from (recur.c,mrca.c) 5.1.pl19 27.04.2003 - recursive Alg. (recur.c) fixed: edge cluster has not to be reconstructed after adding new leaves only updated. - debug output removed from recur.c, split.c - MRCA-based (mrca.c) finished 5.1.pl18 26.04.2003 - recursive (recur.c) finished TODO: remove debug output - MRCA (mrca.c) startet 5.1.pl17 25.04.2003 - split-based (split.c) finished TODO: remove debug output - recursive (recur.c) startet 5.1.pl16 22.04.2003 - orig pstep alg: updating of edgemap outsourced to updateedgemap_orig - writeOTU_orig, writetree_orig, resetedgeinfo_orig, minimumedgeinfo_orig: _orig removed, since independent of algorithm type - onepstep: _orig added (onepstep_orig) - time check/status output moved to checktime routine. added to ml step of parallel version - split.c temporarily added to release 5.1.pl15 18.04.2003 - trueID dependent procedures 'de-trueID-ed' trueID saved in the tips of the tree. 5.1.pl14 10.04.2003 - consensus stuff moved to consensus.h/.c - unique tree sorting moved to treesort.h/.c - changes to pstep-split.h/.c - changed names of procedures using trueID to *_trueID 5.1.pl13 07.04.2003 - subsetmatr.[hc] added to process missing data analyses. (old version, functions in puzzle2) - deglobalized: guessdatatype, readsequencefile, getsizesites, initid, getseqs removed obsolete: getdataset - moved: output of taxa after input - computation of Maxbrnch moved from readsequencefile to inputandinit - readsubsetfile, permutetaxa_ss added, '-rssm' works - empty quartets fixed in checkquartet missing data -> OK, HALT error otherwise 5.1.pl12 04.04.2003 - tests: check-qp-clock regenerated, changes in Makefile.am and template-test - obsolete stuff removed: global trueID_orig + alloc, inittree_orig/freetree_orig from PP_SendDoPermutBlock PP_slave_do_puzzling (ppuzzle), global _orig variables (pstep), makenewsplitentries (old), kh_test (old) - column variable in tree output routines deglobalized - copyright headers added to pstep.[hc] - pstep copied to pstep-{split | mrca | recursive} - implementation of pstep-split.[ch] started (done: structure/init, todo: remove _orig stuff) 5.1.pl11 03.04.2003 - tests/Makefile.am: 'build-puzzle failed' fixed - some changes in test script template - cleanup: removed obsolete routines - puzzle module: makenewsplitentriesnew - ppuzzle module: PP_do_puzzling, PP_SendPermut, PP_RecvPermut, PP_SendSplits, PP_RecvSplits - deglobalized: makenewsplitentries, makepart, computebiparts, copysplit - parallel puzzling step based on allpstep, onepstep - time check/status output added to parallel version (inaccurate since current slave progress not known) - TIMECHECK_INTERVAL for setting time interval of status output in ML/puzzling step - Header when printing 1 PAM rate matrix (-printrmat) - final pstep copied to pstep-{split | mrca | recursive} 5.1.pl10 02.04.2003 - tests/Makefile.am fixed (TODO: build-puzzle.test) - Dates/Version adjusted: April 2003/TREE-PUZZLE 5.2 - Dates/Version fixed in doc/*.html, doc/*.tex - number added to outgroup(menu)/sequence(start) output - Time measurement only done after each completed intermediate tree to reduce the the number from O(Numtrial*n^4) to O(Numtrial) -> less overhead, but 15min met less accurate. - quartet support output for splits added in writeoutputfile for later use (TODO: '#if0'ed) - (sequential) puzzling step moved from puzzle1.c to pstep.c: allpstep, onepstep TODO: parallel puzzling step in ppuzzle.c (works but with old PP_slave_do_puzzling) 5.1.pl9 31.03.2003 - consensus construction added to menu - support value computation fixed for phylip tree, wrong divisor used in consensus - test directory/Makefile.am/tests created (make check) 5.1.pl8 30.03.2003 - puzzling step proc's: most variables 'deglobalized' 5.1.pl7 26.03.2003 - original puzzling step out-sourced to pstep-orig.c and pstep-orig.h pstep.c, pstep.h (and above) added to Makefile.am 5.1.pl6 25.03.2003 - '-usebranch' option added fr later use - 'SONJA' added for external parameter estimation 5.1.pl5 24.03.2003 - ml branch length estimation added to consensus option (todo: plausibility check - is tree file available) - output for reportfile fixed - output of likelihood to clocklike tree in treefile added/fixed 5.1.pl4 21.03.2003 - consensus option added to compute usertree consensus (only consensus is computed and printed to stdin) - usertreefile PREFIX fixed 5.1.pl3 20.03.2003 - TP_MAX_EXP_DIFF=b-a>0 introduced, such that (1.0+exp(a-b) == 1.0) to avoid the computation as well as possible FPE, when a-b gets very small. - flag '-prefix=XXX' added: use 'XXX' as filename prefix instead of 'Infilename' 5.1.pl2 05.12.2002 - PP_Finalized before exit in parallel programs. 5.1.pl1 05.12.2002 - FPE in Brent's algorithm fixed: ()/0, when x=w=v. 5.1 05.11.2002 - Version 5.1 !!!
2010-09-19Update nut to 15.8.obache4-16/+15
Based on PR#43776 by Kamel Derouiche for 15.7. What's new in nut 15.8: * This release updates the USDA database to include some data corrections for milk. * The program's initial data load is now considerably faster. What's new in nut 15.7: * This version includes an improvement to the automatic calorie tool to make it better able to hold fat mass or lean mass constant. * Also, there is now a facility to explicitly set the ratio between linoleic and alpha-linolenic acids. What's new in nut 15.0: * This release introduces the new USDA Nutrient Database SR22 and allows current nut installations to have their existing meal records reinterpreted with the new database. What's new in nut 14.5a: * The new feature "Weight Log Regression" does not tell you what you weigh; what it does is apply linear regression to a series of daily weight and body fat percentage entries to smooth out the random noise and tell you which direction your weight is trending, how fast it is going there, and how much of the change is lean or fat.
2010-09-19Update lucy to 1.20.obache2-8/+13
Based on PR#43777 by Kamel Derouiche, with some clean up by me. Version 1.20, 9/3/2008. This version fixes a bug that caused lucy to fail when there was too much information on the FASTA header lines in the input files. Lucy had a 256 character buffer for reading lines from the input files. If any FASTA header lines were longer than 256 characters, the remaining characters would get read as part of the FASTA sequence. The solution implemented in this version is simply to increase the buffer size to 4096 characters. While that still leaves the potential for the same error to occur with extremely long header lines, the limitation that this entails seems reasonable, and this should fix the problem for all pratical purposes. --------------------------------------------------------------------- Version 1.19, 12/30/2003. This version fixes a bug that could cause sequences to be rejected incorrectly in the vector detection step (phase 6). Because of the way that lucy compares "tags" in the target sequence with "tags" in the vector sequence, some bases in the target sequence could get counted more than once in the tally of bases that match the vector sequence. In rare instances, this could cause the sequence to exceed the minimum threshold for rejection, as a result of random sequence similarity. The reporting of the CLB range in the -debug output file has also been changed. If the CLB range begins with the first base of the sequence, then the left coordinate of the CLB range will be reported as 1 (instead of 0). The range "CLB 0 0" still indicates an empty CLB range.
2010-09-03Update to GROMACS 4.5.1asau10-267/+548
GROMACS 4.5.1 is bug fix release. Release notes for 4.5 New features * Pencil decomposition of the reciprocal space PME grid to improve scaling. This reduces the amount of communication for high parallelization and improves load balancing with up to 40% overall performance improvement for large systems. * Memory usage is improved for very large systems, allowing simulations of >100 million atoms. * Running on a multi-core node now uses thread-based parallelization to automatically spawn the optimum number of threads in the default build. MPI is now only required for parallelization over the network. * Domain decomposition can now also be used without periodic boundary conditions * GPU acceleration support on NVIDIA cards. This first release with GPU support based on OpenMM provides up to an order of magnitude faster performance for implicit solvent simulations, but PME simulations are about as fast as on a high-end CPU. * Check-pointing is made more secure:MD5sum are used to verify that all files are correctly in-place before a simulation is appended. Output file appending at continuation is turned on by default. * Increased tolerance for networked file system failures and cluster node crashes: checkpoint handling is safer and mdrun forces file system cache flushes during checkpoints. * Full CMake support. After the 4.5 release we will be switching the default build tool from autoconf to cmake, and possibly deprecate autoconf in the future. * Full support for seven AMBER force fields in the standard distribution, with default Amber names. We also include the recent Amber99sb-ildn in the distribution. * Support for CHARMM27, including cmap for dihedrals * Efficient Generalized-Born implicit solvent support including the Still/HCT/OBC-models to compute the Born radii, a novel way of tabulating the generalized Born-interaction formula for greater speed, and optimized SSE-routines in both single and double precision. * Highly efficient all-vs-all assembly kernels for both vanilla and generalized born interactions, in both single and double precision. * Much better support for nucleic acid simulations, including automatic handling by pdb2gmx. * Support for Velocity-Verlet integrators for reversible T- and P-coupling; MTTK pressure control integrators; Nose-Hoover chains. * Symplectic Trotter Leap-Frog integrator for twin-range non-bonded interactions. * Support for Bennet acceptance ratio calculations through direct calculation of Hamiltonian differences during the simulation. * File formats: All GROMACS tools can now read any VMD supported trajectory format, without converting trajectory first. (VMD libraries are required). * pdb2gmx now retains the residue numbers from the input, mdrun and all tools use these original numbers. New tools * g_bar: Bennett acceptance ratio (BAR) free energy calculations, including automatic error estimates and phase space overlap measures. * g_rdf was a little bit enhanced that structure factors can be calculated for any system, by supplying the necessary data via sfactor.dat. Most of the common atomtypes are already contained, but everybody who needs more freedom can enhance the table * g_select: Library support for "dynamic index groups" based on textual selections (experimental feature). See the tool g_select, the included template.c, or Doxygen documentation for information on how to write analysis tools using the library. Existing tools have not (yet) been converted. * g_tune_pme: For a given number of processes or threads this tool systematically times mdrun with various numbers of PME-only nodes and determines which setting is fastest. It also checks whether performance can be enhanced by shifting load between the real and the reciprocal space part of the Ewald sum. * g_membed: a very convenient utility for rapidly embedding membrane proteins into equilibrated lipid bilayers * g_pme_error: estimates the error of the electrostatic forces if using the SPME algorithm. TO be incorporated in g_tune_pme Changes that might affect your results * grompp by default sets the new nstcalcenergy parameter equal to nstlist, this has no effect on the integration, only on the energy averages stored in ener.edr * grompp by default sets the new nsttcouple parameter equal to nstlist, this means T-coupling is done less frequently; grompp checks if tau_t is large enough * grompp by default sets the new nstpcouple parameter equal to nstlist, this means P-coupling is done less frequently; grompp checks if tau_p is large enough * mdrun results with old tpr files with twin-range non-bonded interactions will be different, because of the new symplectic integrator * for free-energy calculations sc-sigma now also sets the minimum soft-core sigma (old tpr files retain the old behavior, which can be enforced by setting the env.var. GMX_SCSIGMA_MIN to 0)
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-10 17:27:09 +0000