[gmx-users] Segmentation fault and PCA Analysis

Ahmed Mashaly mashaly_1988 at yahoo.com
Thu Jul 19 08:09:33 CEST 2018

Dear users,
I am trying to align my trajectory to an average structure pdb, the problem is that I have "Segmentation fault (core dumped)" while taking this pdb as a reference structure, while it worked with the em.tpr file ... I also tried to extract the pdb from the that em.tpr using gmx editconf and when I used it as a reference I faced the same problem, so I guess the peoblem with the pdb format ... Any suggestions?
Another question about PCA, is there a way to do dot product in GROMACS?
Kind regards,Ahmed

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