[gmx-users] Box Exploding Error

Mark Abraham Mark.Abraham at anu.edu.au
Sun Jan 11 00:47:26 CET 2009

> Hello All,
> First, for this question I am referring to GROMACS 3.3.3.  I have 
> thoroughly read the archives for errors on why a simulation box might 
> explode.  My simulations require that I bring the N and C terminal ends 
> of a ~20 amino acid peptide as close together as possible.  To do this, 
> I am using the pull code to freeze the C terminus and pull the N 
> Terminus toward it.

I would use normal MD with distance restraints between suitable terminal 
atoms. This is a much simpler approach to this problem.

>  I keep getting the following error during the 
> simulation:
> Back Off! I just backed up md_traj.xtc to ./#md_traj.xtc.1#
> Warning: 1-4 interaction between 5 and 10 at distance 1.480 which is 
> larger than the 1-4 table size 1.000 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

See http://wiki.gromacs.org/index.php/blowing_up

> My question: Is there any way to completely ignore this error, so that 
> the N Terminus is pulled as close as possible to the C Terminus?

That's not your problem. Atoms 5 and 10 are too close because there's 
something unphysical about your model, and anyway these atoms are not 
your terminal pair.

>  I 
> understand that the results in the .pdo file of the pull simulation may 
> be unrealistic, but I simply need to get a peptide structure whose N and 
> C Terminal ends are close together (within .5 nm).  On a side note, are 
> there any suggestions for respectable molecular modeling software with 
> which I may be able to BUILD a circular peptide (i.e. - N and C Terminal 
> ends are brought close together)?  Any help is appreciated.

There are a few links here 
http://wiki.gromacs.org/index.php/Coordinate_File that might help.


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