[gmx-users] Error after Mdrun

Nikit sharan nikit2702 at gmail.com
Fri Feb 20 10:17:27 CET 2009

Dear all,

   I need some help in my simulation. I Put system(dppc bilayer) in a
cubic box then solvated it and made a equlibriation run.There were no
issues till then.But when i proceded  with the production run , the
simulation crashes in no more than 5 or 10 steps leaving an error
message saying ,

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

 And there are warnings like:

  1-4 interactions between 1163 and 1184 at distance 1.026 which is
larger than the 1-4 table size 1 nm, This usually means your system is

 Warning: pressure scaling more than 1%, mu: 2.31762e+27 2.31762e+27 2.31762e+27

    I tried to increase the table size but as I increased this value
the distance always increased together, and I got again the same
warning with different values,  so this didn´t help. I tried energy
minimization further but there also it ends up with

"Steepest Descents converged to machine precision in 166 steps,
but did not reach the requested Fmax < 1e-05.
Potential Energy  = -3.4207141e+05
Maximum force     =  5.0177407e+03 on atom 5265
Norm of force     =  1.3222472e+04

 am getting the energy in a low negative value and also I have already
gone through the mailing list regarding the same issue.But i couldn't
get it clear.

   I am still a begginer in Gromacs, and I really don´t know what
could bethe reason for these errors... It is also the first time that
I am dealing
with molecular dynamics simulation. Someone wrote me that it could
besomething 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

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