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
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