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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
