[gmx-users] simulation crash with GROMOS96 force field

[Vitaly V. Chaban]

Hi all,

I am trying to simulate a small organic molecule (42 atoms with 18
hydrogens among them) in water (SPCE). The force field was generated
with X2TOP utility using GROMOS96 force field. All bonds, pairs,
angles, dihedrals, etc are OK and the system runs OK but sometimes it
craches producing several PDB files and CORE files. The message in the
standart output is:

t = 122.523 ps: Water molecule starting at atom 2497 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Warning: 1-4 interaction between 62 and 80 at distance
2653175545629928960.000 which is larger than the 1-4 table size 2.450
nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

t = 122.524 ps: Water molecule starting at atom 1009 can not be settled.
Check for bad contacts and/or reduce the timestep.

t = 122.524 ps: Water molecule starting at atom 1693 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates

The timestep is 1fs, the temperature varies from 25C up to 70C,
barostat is turned on. If I reduce the timestep to 0.25fs, the problem
does not appear fortunately but I would like to keep it equal to 1fs.
I am sure the problem is with an organic molecule because it doesn't
appear with SPCE water only. In the organic molecule nexcl=3 and all
angles are defined well. Trying LINCS instead, I got a big number of
warnings (>1000).

What can be wrong with my force field (generated by X2TOP) else ?

Thanks in advance.

-- 
Vitaly V. Chaban, Ph.D.
http://www-rmn.univer.kharkov.ua/chaban.html