QM/MM simulation crashes with segmentation fault when running it a second time

QM/MM for Biomolecular Simulation
1

Dear all,

I am trying to run QM/MM simulations of an enzyme with an cysteine bound ferric heme in the centre and I came across a strange problem with my simulations: I did run an energy minimisation once that completed, but when I restart it a second time the simulation crashes with segmentation fault error.
Since I am quite new to QM/MM simulations I am not sure if there is a problem with my input or if the gromacs + CP2K interface on the cluster has a bug.

I did create a folder in my owncloud with all the input files I am using, so you can have a look at my parameters. I would be very glad about any tip on my issue.

Best,
Hanna

2

Hi, Try to put more atoms into QM part. For Cysteine at least S-CH2 should be included

3

I included the atoms you suggested and now it kinda works. At least when I am using the BLYP functional. Strangely I still get segmentation faults when I am using PBE. I did just try it as a test but do you have any guess why this is happening?