[gmx-users] Segmentation fault using gmx solvent

[Mark Abraham]

Hi,

gmx solvate shouldn't segfault based on a minor change to the input
coordinates, so it's probably a bug to look into. Please open an issue at
https://redmine.gromacs.org and attach inputs with a failing gmx command,
and someone can likely provide some insight!

Mark

On Thu, 14 Nov 2019 at 19:19, Anthony Nash <anthony.nash at ndcn.ox.ac.uk>
wrote:

>
> 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/
>
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