[gmx-users] Infinite CNT

Daniel Cheong dcheong at ihpc.a-star.edu.sg
Tue Apr 24 09:43:54 CEST 2007

Hi all,

I am trying to do a simulation of an infinite CNT.  I have generated the 
coordinates using tubegen and use x2top to generate the topology.  
Initially I kept getting the error that the forcefield was not found for 
a carbon bonded to 2 atoms.  After adding to the .n2t file, x2top 
successfully generated a topology file.  i replicated the CNT along the 
tube axis several times and increased the box dimensions along the other 
axes so that they will be larger than the cut-offs.  However when I run 
the MD simulation, it keeps giving the error that the 1-4 interactions 
distance between certain atoms are larger than the table size and then 
gives a segmentation fault.  i tried increasing the table-extension but 
still get the segmentation fault.  I have looked through the archives 
and have found some posts on infinite CNTs.  But i can't find a solution 
to my problem.   If anyone can give any help or advice, it would be much 


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