Poojari, Chetan wrote:
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.
Typically, when an old version works and the new version is broken, a bug is at
fault. If you consistently observe this behavior with other systems or smaller
systems (to rule out simply running out of memory, etc), then please file a bug
report on redmine.gromacs.org with all necessary input files to reproduce the
problem.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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