[gmx-users] Force a gromacs tool to write step-by-step a result in a xvg file

intra\sa175950 stephane.abel at cea.fr
Tue Sep 6 12:12:36 CEST 2011

Dear All 


I use the g_clustersize to examine the cluster decay vs. time during the
aggregation process of glycolipids into a micelle with the following


$WORKDIR/gromacs-4.5.3/bin/g_clustsize_mpi -f *.xtc -s run_1.tpr -mc
bDM-AMBER99SB-ILDN-Self_b_cluster.xvg -nc
bDM-AMBER99SB-ILDN-Self_b_N_cluster.xvg -b 102000 -e 102000 -dt 4 -tu ps -n


Unfortunately, the program stops with the following error after several




Program g_clustsize_mpi, VERSION 4.5.3

Source code file: matio.c, line: 561


Fatal error:

Lo: 0.000000, Mid: 1.000000, Hi: 1.000000



I know that this error comes because I have in my system only one cluster of
constant size in my system.


Unfortunately, when this error appears g_clustsize_mpi stops and no results
for the preceding steps are written in the corresponding xvg files.  So it
is possible to force g_clustersize (and any others gromacs tools) to write
step-by-step a calculation in a *.xvg file.


Thank you in advance for your help 



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