[gmx-users] g_covar : segmentation fault

[Poojari, Chetan]

Hi,

I am doing Dihedral PCA and followed the steps as mentioned in the Gromacs documentation http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA

Below are the commands i used:

1) I generated index file for chosen dihedral angles.

2)  g_angle -f 100ns_noPBC.xtc -n dangle.ndx -or dangle.trr -type dihedral

3) trjconv -s md_100ns.tpr -f dangle.trr -o resized.gro -n covar.ndx -e 0

4) g_covar -f dangle.trr -n covar.ndx -ascii -xpm -nofit -nomwa -noref -nopbc -s resized.gro


While running the command in step 4, it runs for sometime and then i get segmentation fault. I was doing these in Gromacs 4.5.4 package.


When i switched to Gromacs 4.0.7 package and repeated the steps, i ran successfully without any errors.

Please can I know what changes can be done to the commands I have used so that i can get it running with Gromacs 4.5.4 package as well.


Kind regards,
chetan

------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------

Besuchen Sie uns auf unserem neuen Webauftritt unter www.fz-juelich.de