[gmx-users] Segmentation fault using gmx solvent

[Anthony Nash]

Hi all,

I've been fighting a particularly painful problem with a system I'm building in Gromacs.

gmx mdrun (grompp worked on the system) has been throwing a segmentation fault on my collagen system in a vacuum. Shortly after, I tried gmx solvate but that too was also throwing a segmentation fault. I tried the same steps over three different Gromacs distributions and they all failed ruling out any issues with Gromacs versions.

My system is a set of collagen fibrils (little in the way of water/voids) built from a crystal structure. I've had the system running before as a wildtype (just as is) and after I added post-translational modified (PTM) amino acids. That was a year ago. This week I've added a new PTM amino acid to the *final* frame of the wildtype simulation. Adding the PTM amino acid went through fine with pdb2gmx, make_ndx, editconf, all working completely ok.

Unfortunately, gmx solvate fails with a segmentation fault and no other indication of the problem. As I built the system from a final mdrun frame, individual peptides had crossed the unit cell (leaving voids in the main unit cell) and the final geometry kept those peptides 'whole'. Suspecting that gmx solvate can't solvate a space in the unit cell which is actually occupied across its period boundary conditions (as a guess), I executed trjconv -pbc atom to put all the content back into the original cell. However, I'm still getting a segmentation fault even when I restore the pbcs.

If I remove everything put a few amino acids, gmx solvate works. Further, VMD crashes when it tries to render either pre or post trjconv -pbc atom. I can only guess that my structure (in the .gro file) is causing gmx solvate to crash, but I'm really not sure why.

Suggestions are hugely appreciated. Please let me know what information I can provide to help.

Thanks
Anthony


Kind regards
Dr Anthony Nash PhD MRSC

Senior Research Scientist
Nuffield Department of Clinical Neurosciences
RMCR Kellogg College
University of Oxford
http://www.kellogg.ox.ac.uk/