[gmx-users] Box Exploding Error

[VENKATESH HARIHARAN]

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 keep getting the
following error during the simulation:


 
  Normal
  0
  
  
  
  
  false
  false
  false
  
  EN-US
  X-NONE
  X-NONE
  
   
   
   
   
   
   
   
   
   
   
   
  
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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




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?  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.

______________________________

Venkatesh Hariharan
The Pennsylvania State University
Schreyer Honors College
Undergraduate - Bioengineering

"You must be the change you wish to see in the world."
--Mohandas Karamchand Gandhi


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