Hi Mark,
Works perfectly...
Thanks,
Craig
Craig Kitchen
Department of Chemistry
University of Cambridge
Lensfield Road
Cambridge
CB2 1EW
UK
On 26/03/11, Craig Kitchen <ck...@cam.ac.uk> wrote:
Dear All,
When running g_cluster on a file generated with g_mdmat I receive a
segmentation fault. I have tried different versions of Gromacs (4.0.5 and
4.5.3) on different workstations with both large and small matrices - all
without success.
Good trouble-shooting and report. You'd likely have been asked to check a
recent version and with a small matrix :-)
This was a two-part bug - a clean-up function was called when the
corresponding initialization hadn't been called, and that clean-up function
assumed that initialization had happened. I fixed both in git.
You can work around this by hacking in src/tools/gmx_cluster.c. Around line
1260 there will be code like
if (bPBC) {
gmx_rmpbc_done(gpbc);
}
which you should move one line up (inside a set of braces that mean the
clean-up is called only after initialization occurs). Don't worry about the
indenting.
Mark
I am calling g_cluster with:
g_cluster -dm dmat_1.xpm -cutoff 3.4 -g cluster_1.log
Whereupon I receive the error:
Using linkage method for clustering
Reading rms distance matrix 100%
Segmentation fault
The distance matrix (dmat_1.xpm) was generated with:
g_mdmat -f onlyba.gro -s onlyba.gro -t 4.0 -mean dmat_1.xpm
The configuration (onlyba.gro) and matrix file (dmat_1.xpm) are attached
(and since they are short also pasted below).
Any help on this would be greatly appreciated!
Regards,
Craig
Craig Kitchen
Department of Chemistry
University of Cambridge
Lensfield Road
Cambridge
CB2 1EW
UK
Generated by trjconv : Coarse-Grained Model of EAS Barrels and Loop
Residues (including bonds) t= 0.00000
10
1BA BA 1 44.780 21.592 37.304 0.0067 0.0035 0.0073
29BA BA 2 12.191 38.323 0.704 -0.0084 0.0108 -0.0014
57BA BA 3 2.092 9.298 47.957 0.0053 -0.0144 0.0053
85BA BA 4 15.664 33.182 25.406 0.0291 -0.0067 -0.0069
113BA BA 5 47.194 32.613 24.031 -0.0146 -0.0132 0.0184
141BA BA 6 11.731 25.247 11.921 -0.0100 -0.0049 0.0025
169BA BA 7 33.751 20.349 25.599 -0.0103 -0.0131 0.0078
197BA BA 8 2.467 11.277 47.988 -0.0063 0.0188 -0.0001
225BA BA 9 25.948 26.283 35.007 0.0191 0.0058 0.0047
253BA BA 10 26.103 27.621 36.697 -0.0057 0.0281 -0.0110
48.00000 48.00000 48.00000
/* XPM */
/* Generated by g_mdmat */
/* This file can be converted to EPS by the GROMACS program xpm2ps */
/* title: "Mean smallest distance" */
/* legend: "Distance (nm)" */
/* x-label: "Residue Index" */
/* y-label: "Residue Index" */
/* type: "Continuous" */
static char *gromacs_xpm[] = {
"10 10 40 1",
"A c #FFFFFF " /* "0" */,
"B c #F8F8F8 " /* "0.103" */,
"C c #F2F2F2 " /* "0.205" */,
"D c #EBEBEB " /* "0.308" */,
"E c #E5E5E5 " /* "0.41" */,
"F c #DEDEDE " /* "0.513" */,
"G c #D8D8D8 " /* "0.615" */,
"H c #D1D1D1 " /* "0.718" */,
"I c #CBCBCB " /* "0.821" */,
"J c #C4C4C4 " /* "0.923" */,
"K c #BEBEBE " /* "1.03" */,
"L c #B7B7B7 " /* "1.13" */,
"M c #B1B1B1 " /* "1.23" */,
"N c #AAAAAA " /* "1.33" */,
"O c #A3A3A3 " /* "1.44" */,
"P c #9D9D9D " /* "1.54" */,
"Q c #969696 " /* "1.64" */,
"R c #909090 " /* "1.74" */,
"S c #898989 " /* "1.85" */,
"T c #838383 " /* "1.95" */,
"U c #7C7C7C " /* "2.05" */,
"V c #767676 " /* "2.15" */,
"W c #6F6F6F " /* "2.26" */,
"X c #696969 " /* "2.36" */,
"Y c #626262 " /* "2.46" */,
"Z c #5C5C5C " /* "2.56" */,
"a c #555555 " /* "2.67" */,
"b c #4E4E4E " /* "2.77" */,
"c c #484848 " /* "2.87" */,
"d c #414141 " /* "2.97" */,
"e c #3B3B3B " /* "3.08" */,
"f c #343434 " /* "3.18" */,
"g c #2E2E2E " /* "3.28" */,
"h c #272727 " /* "3.38" */,
"i c #212121 " /* "3.49" */,
"j c #1A1A1A " /* "3.59" */,
"k c #141414 " /* "3.69" */,
"l c #0D0D0D " /* "3.79" */,
"m c #070707 " /* "3.9" */,
"n c #000000 " /* "4" */,
/* x-axis: 1 2 3 4 5 6 7 8 9 10 */
/* y-axis: 1 2 3 4 5 6 7 8 9 10 */
"nnnnnnnnVA",
"nnnnnnnnAV",
"nnUnnnnAnn",
"nnnnnnAnnn",
"nnnnnAnnnn",
"nnnnAnnnnn",
"nnnAnnnnnn",
"nnAnnnnUnn",
"nAnnnnnnnn",
"Annnnnnnnn"
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