Commit 575aadb9 authored by Nicholas Breen's avatar Nicholas Breen

New patch 05_autoconf_gsl corrects failure to set LIBS=-lgsl properly in...

New patch 05_autoconf_gsl corrects failure to set LIBS=-lgsl properly in configure step; g_kinetics(1) man page updated
parent 347e4786
gromacs (3.3.3-3) UNRELEASED; urgency=low
gromacs (3.3.3-3) unstable; urgency=low
[ Daniel Leidert ]
* debian/gromacs-data.doc-base (Section): Fixed accordingly to latest
......@@ -10,8 +10,13 @@ gromacs (3.3.3-3) UNRELEASED; urgency=low
* debian/control: Update Standards-Version to 3.8.0.
* debian/rules: Remove obsolete and now-inaccurate comment about
parallel builds. Remove duplicated dh_installdeb call.
* debian/man/g_kinetics.1: Update documentation.
* debian/patches/05_autoconf_gsl.dpatch: libgsl was not properly
detected by autoconf when the test didn't also link libgslcblas,
rendering the g_kinetics program unusable. This changes the test
to pass along LIBS appropriately.
-- Daniel Leidert (dale) <> Sun, 09 Mar 2008 22:36:10 +0100
-- Nicholas Breen <> Wed, 20 Aug 2008 11:55:39 -0700
gromacs (3.3.3-2) unstable; urgency=low
.TH "G_KINETICS" "1" "3 Mar 2008" "GROMACS suite, Version 3.3"
.TH "G_KINETICS" "1" "20 Aug 2008" "GROMACS suite, Version 3.3"
g_kinetics \- estimate rate constants
.B g_kinetics
.B \-[no]h
.B [other options...]
.BI "\-f" " temp.xvg "
.BI "\-d" " data.xvg "
.BI "\-o" " ft_all.xvg "
.BI "\-g" " remd.log "
.BI "\-m" " melt.xvg "
.I [other options...]
.B g_kinetics
......@@ -32,12 +36,65 @@ The program can also be used with continuous variables (by setting
studied. This is very much a work in progress and hence the manual
(this information) is lagging behind somewhat.
Option Filename Type Description
-f temp.xvg Input xvgr/xmgr file
-d data.xvg Input xvgr/xmgr file
-d2 data2.xvg Input, Opt. xvgr/xmgr file
-o ft_all.xvg Output xvgr/xmgr file
-o2 it_all.xvg Output, Opt. xvgr/xmgr file
-o3 ft_repl.xvg Output, Opt. xvgr/xmgr file
-ee err_est.xvg Output, Opt. xvgr/xmgr file
-g remd.log Output Log file
-m melt.xvg Output xvgr/xmgr file
.BI "\-[no]h
Print help info and quit (default: \fIno\fP).
Other options are available but not currently well documented.
Option Type Value Description
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 19 Set the nicelevel
-tu enum ps Time unit: ps, fs, ns, us, ms or s
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-[no]time bool yes Expect a time in the input
-b real 0 First time to read from set
-e real 0 Last time to read from set
-bfit real -1 Time to start the fit from
-efit real -1 Time to end the fit
-T real 298.15 Reference temperature for computing rate constants
-n int 1 Read data for # replicas. Only necessary when
files are written in xmgrace format using @type
and & as delimiters.
-cut real 0.2 Cut-off (max) value for regarding a structure as
-ucut real 0 Cut-off (max) value for regarding a structure as
intermediate (if not folded)
-euf real 10 Initial guess for energy of activation for
folding (kJ/mole)
-efu real 30 Initial guess for energy of activation for
unfolding (kJ/mole)
-ei real 10 Initial guess for energy of activation for
intermediates (kJ/mole)
-maxiter int 100 Max number of iterations
-[no]back bool yes Take the back reaction into account
-tol real 0.001 Absolute tolerance for convergence of the Nelder
and Mead simplex algorithm
-skip int 0 Skip points in the output xvg file
-[no]split bool yes Estimate error by splitting the number of
replicas in two and refitting
-[no]sum bool yes Average folding before computing chi^2
-[no]discrete bool yes Use a discrete folding criterium (F <-> U) or a
continuous one
-mult int 1 Factor to multiply the data with before
.BR gromacs (7)
#! /bin/sh /usr/share/dpatch/dpatch-run
## 04_autoconf_mpisuffix.dpatch by Nicholas Breen <>
## All lines beginning with `## DP:' are a description of the patch.
## DP: The test for libgsl fails when libgslcblas is not also linked,
## DP: which occurs when LIBS from earlier tests are not passed down.
## DP: Splitting the AC_CHECK_LIB calls apart solves this.
## DP: Last updated 20-Aug-2008 for upstream release 3.3.3
--- gromacs-3.3.3_orig/ 2008-08-20 11:37:57.000000000 -0700
+++ gromacs-3.3.3/ 2008-08-20 11:37:27.000000000 -0700
@@ -529,11 +529,11 @@
if test "$with_gsl" = "yes"; then
- AC_CHECK_HEADERS([gsl/gsl_version.h],[
+ AC_CHECK_HEADERS([gsl/gsl_version.h])
# header found, check for libraries
- AC_CHECK_LIB(gslcblas,main,[
+ AC_CHECK_LIB(gslcblas,main)
# gslcblas library found, check main lib
- AC_CHECK_LIB(gsl,main)])])
+ AC_CHECK_LIB(gsl,gsl_blas_dgemm)
......@@ -84,10 +84,10 @@ configure-stamp: patch-stamp
cp -f /usr/share/misc/config.sub config.sub
-test -r /usr/share/misc/config.guess && \
cp -f /usr/share/misc/config.guess config.guess
# patch 04_autoconf_mpisuffix changes, requiring a fresh autotools pass
# patches 04_autoconf_mpisuffix & 05_autoconf_gsl change, requiring a fresh autotools pass
aclocal && \
autoconf && \
automake-1.10 || automake
# -dp is the place for double-precision builds
(mkdir -p build/basic; cd build/basic; ../../configure $(COMMON_CONFIG_PARAMS))
(mkdir -p build/basic-dp; cd build/basic-dp; ../../configure $(COMMON_CONFIG_PARAMS) --program-suffix=_d --enable-double)
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