[gmx-users] about segmentation fault related with gmx trjconv

[lazaro monteserin]

Dear gromacs users,

Dear Mathias

I have a problem when I try to generate the reference file .gro to run gmx
covar doing the dPCA in gromacs:

Note: first of all my system has 32 atoms.

1) $GMX/gmx angle -f md_0_100.xtc -n angle.ndx -or angle.trr -type dihedral
 2) I modified the angle.ndx in order to only have one group:
------------------------------------------------
*Head of file:*
[Phi and Psi]
1 2 4 5 …..(all the dihedral angles)
------------------------------------------------
It says a note: "There are 99 dihedrals. Will fill 66 atom positions with
cos/sin"

3) So I created my covar.ndx with 66 elements.

4) Then I run: gmx trjconv -f angle.trr -s md_0_100.tpr -o resized.gro -n
covar.ndx -fit none -e 10000, where 10000 is in ps (my simulation was 10ns).
But then I get the following error: *" line 31: 56948 Segmentation fault
(core dumped) $GMX/gmx trjconv -f angle.trr -s md_0_100.tpr -o resized.gro
-n covar.ndx -e 10000" *

Any idea why is doing segmentation fault?

Also notice that my molecule has 32 atoms and is not a typical protein or
aminoacid. It is a nucleotide.

Kindly,
 Lazaro