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.n...@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/ > > -- > 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. > -- 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.