[gmx-users] mdrun error

Mark Abraham Mark.Abraham at anu.edu.au
Wed Feb 25 08:32:29 CET 2009

supti mukherjee wrote:
> Dear all,
> I am doing a protein simulation for 20ns in single processor machine. 

You may wish to avoid using MPI versions of GROMACS on a 
single-processor machine.

> after 11.1ns when I am trying to rerun mdrun its coming out with the 
> following error.
> --------------------------------------
> Inner product between old and new vector <= 0.0!
> constraint #0 atoms 1 and 2
> Warning: 1-4 interaction between 1 and 7 at distance inf which is larger 
> than the 1-4 table size 2.400 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
> MPI process rank 0 (n0, p20175) caught a SIGSEGV.
> -----------------------------
> Can anybody please give me some clue to solve this?



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