[gmx-users] Fwd: segmentation fault on gpus

ram bio rmbio861 at gmail.com
Mon Jun 23 23:53:53 CEST 2014

Dear Gromacs Users,

I have been trying to simulate protein-ligand complex using gromacs
versions that use verlet cutoff scheme on gpus.

These are some of the issues that i could resolve, and any kind of
suggestion or help is appreciated.

1. With gromacs 4.6.5 i could simulate crystal structure from pdb but not
modelled protein with ligand always ended up in segmentation fault. The MD
run during equillibration runs for gew thousands of steps and errors out as
segmentation fault, so i have to rerun using previous cpt file, for a run
of 2ns to complete i have to rerun it for 7-10 times.

So if the the system id not minimized, why would it go into rerun?

2. I though it could be a bug and used 4.6.3 and 5.0 release, with this
trial i could equillibrate just modelled protein but not with the
protein-ligand complex. The same error occurs as i mentioned above with
protein-ligand complex...

I am attaching my mdp file and the minimized structure that i am using for

Please let me know your suggestions.

Thanks and Regards,

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