[gmx-users] table extension problem

Fernando Mattio mattiofer at gmail.com
Thu Nov 24 14:46:19 CET 2005

Dear Gromacs users,

When I tried to run my simulation (that consists of a box with 55969 mol of
solvent,  one protein and  1860  water molecules to be treated as ice so I
applied the frozen group option to keep it´s  original coordenations)  with
just 26 of my "ice molecules"  everything went ok, but when I tried to run
with all of them I got fatal errors related to table extension, so it
crashed always on step 2.
As an example:

Step 2  Warning: pressure scaling more than 1%, mu: 8.23596e+14 8.23596e+14

Back Off! I just backed up step1.pdb to ./#step1.pdb.11#

Back Off! I just backed up step2.pdb to ./#step2.pdb.5#
Wrote pdb files with previous and current coordinates
Program mdrun, VERSION 3.3
Source code file: nsgrid.c, line: 220

Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.

Also there were warnings like:

Back Off! I just backed up step0.pdb to ./#step0.pdb.10#
Wrote pdb files with previous and current coordinates
step 0Warning: 1-4 interaction between 66 and 72 at distance
335518.228which is larger than the 1-4 table size
20000.000 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

Ok, at this point I changed the table extension from 1 nm to 2 nm, but again
I got again this kind of error... Then I changed to 20nm, then 200 nm...
then 20000nm to see what happens, and always I got the same problem! And 1-4
interactions distances between atoms  always increased in my tries (the last
one as you can see is 335518.228 !!!).
So when I increase my table extension (as suggested by the Gromacs message),
the distances always increases together and it fails again... By this way I
will never solve the problem...

So if anyone has ideas about how to solve it (maybe changing other
parameters) or even observations about it, it would be nice if you can share
these informations with me. Thank you very much in advantage.
And best regards,
Fernando Mattio
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