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.
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.xpmThe 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 UKGenerated 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"
onlyba.gro
Description: onlyba.gro
dmat_1.xpm
Description: dmat_1.xpm
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