[gmx-users] Segmentation Fault - Water on Substrate

[Diez Fernandez, Amanda]

Dear Gromacs users,

I am want to simulate water on a  substrate.
I have a water.pdb file with the coordinates of a cuboid of water and a substrate.pdb file with the coordinates of the substrate. The box dimensions along the x and y directions are identical for both  files.
I run two simulations to minimise both structures separately. I get no error, meaning the topology file must be correct (is this a correct assumption?) This also ensures that all atoms in the minimised.pdb files are within the box I have specified  (as opposed to before, when some atoms were slightly outside).
I then have a script to merge both minimised .pdb files.
I minimise the system and get a segmentation fault:

40783 Segmentation fault

Further, in the file.log I get:


Steepest Descents:

   Tolerance (Fmax)   =  6.00000e+01

   Number of steps    =       100000

           Step           Time         Lambda

              0        0.00000        0.00000


   Energies (kJ/mol)

           Bond          Angle          LJ-14     Coulomb-14        LJ (SR)

    1.36501e+04    6.58753e+04    4.22206e+04   -1.70332e+06           -nan

   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)

    1.18196e+06    2.65781e+03           -nan           -nan



I have visualised the input merged.pdb file and have also checked the minimum and maximum coordinates of water and substrate and I am sure there is no atom overlap. In fact, water and substrate atoms are separate by more than 3A.  ( I have also tried previously with smaller separations).

What could else could I check?

Thanks,
Amanda