Segmentation fault when analyze a trajectory which does not have same number of atoms as the .tpr file
So far I experienced that several tools trjconv, g_rms, grmsf, g_covar, g_anaeig crash with a segmentation fault if the trajectory read in does not have the same atom number as the atom number in the .tpr file. I realized it when I tried to analyze my trajectories of protein simulation after I removed the water molecules from them. It seems to be a systematic problem. I can do the same analysis without any problems with the older version of gromacs tools, i. e. version 4.0.7. The older version would carry out the calculation normally but with a warning that the trajectory does not have the same number of atoms as the total atom numbers specified in the .tpr file.
#2 Updated by Xiaohu Hu over 9 years ago
Hi, I used trjconv to write out the trajectory from the original trajectory that only contains the protein. If I want to do analysis on this protein-only trajectory combined with the .tpr file, then it crashes with a segmentation fault. But it works perfectly with older version of the gromacs tools. I will upload some example files to demonstrate it shortly.
(In reply to comment #1)
Did you remove the water from the trajectory? That should work, but not the
other way around. Please upload a small example with only a few frames in the
trajectory and give an exact command line that allows us to reproduce it.
#4 Updated by Maria Pechlaner almost 8 years ago
I have the same problem, using gromacs 4.5.5.
It does not happen systematically: I have a number of simulations where the only difference is the starting conformation of my macromolecule, which also leads to slightly varying cell volumes, numbers of ions and water molecules.
I write out the .xtc trajectories without water, and when I run g_rms in some cases I get a segmentation fault after g_rms prints the "WARNING: topology has 78959 atoms, whereas trajectory has 1682", in other cases I don't.
#5 Updated by David van der Spoel almost 8 years ago
- Assignee deleted (
As a rule it is a good idea to have the same number of waters and ions for the same macromolecule.
Are you sure that you use the tpr corresponding to the xtc - with only water removed? Because if the number of ions also changes anything can happen. Please provide examples of short trajectories (two frames is enough) and corresponding tpr file.