[gmx-users] Simulation not running, system exploding.

Fernando Mattio mattiofer at gmail.com
Thu Dec 15 10:01:56 CET 2005

   Hi dear Gromacs users,

   I need some help in my simulation. I am trying to put in a cubic box a
protein next to an ice plane and then i solvate the system and try to run
the simulation. As the pdb2gmx doesnt´ work with water molecules, I
proceeded as the following:
   First  I used  the  pdb2gmx  only  with the protein  to get a  topology
file. Then  I tried to create an .itp file of the  ice molecules, and for
that I used the water model spc.itp (but I changed the nomenclature in the
file, everything that was called SOL I changed and called OHH).
   Later I included this .itp file in the topology file, paying attention to
the number of molecules. After that  I  used editconf to create a box and
genbox to  solvate  the system (From the .gro file with the protein next to
the ice plane). By this way in the topology was included the water molecules
(called SOL) by the .itp file of the water. Then in the parameter file I
tried to establish differences between the ice and water molecules by
applying frozen groups options to the OHH molecules.
   However the funny thing is that when I first used part of the ice plane
(with only 26 molecules that were somehow far away from the protein) the
simulation  finished, but when I  used the whole plane (round 1200
molecules) the simulation crashes in no more than 5 or 10 steps.

   The message is always like this :
   Fatal error: Number of grid cells is zero. Probably the system and box

   And there are warnings like:
   1-4 interactions between 25 and 33 at distance 1,322 which is larger than
the 1-4 table size 1 nm, This usually means your system is exploding.

    I tried to increase the table size but as I increased this value the
distance always increased together, and I got agai the same warning with
different values,  so this didn´t help. I tried also to perform energy
minimization before solvating the system, but something bizarre happened,
part of the ice plane just changed position with the protein... like the
visualization was the same, but water molecules were in the position where
the protein was and the protein was in the position where  these water
molecules were before.

   I tried then to put he whole protein a little bit far away from the plane
to see what happens, and when I runned the simulation (without energy min.)
the same birarre thing happened (part of the plane changed place with the

   I am still a begginer in Gromacs, and I really don´t know what could be
the reason for these errors... It is also the first time that I am dealing
with molecular dynamics simulation. Someone wrote me that it could be
something related to topologies, but i really couldn´t find where the error
was. So I ask for your kindness help. Suggestions and advices will be

   Best regards,
   Fernando Mattio
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