[gmx-users] Infinite CNT

Daniel Cheong dcheong at ihpc.a-star.edu.sg
Tue Apr 24 11:13:49 CEST 2007

Thanks for the reply.

I didn't do regenerate the topology before.  What I did then was change 
the number of CNT "molecules" in the top file to the number of 
replications I made.  However, after seeing your post, I tried 
regenerating the topology with the extended tube, but still get the 
error that the 1-4 interaction distance is larger than the table size, 
and then the segmentation fault.  What I don't quite understand is... in 
the topology that x2top generated, it lists the bonded and 1-4 
interactions in the CNT "unit" that I give it to generate the topology, 
but the topology doesn't specify if the interactions are with itself or 
with its periodic images.  Will Gromacs know to use the minimum image 
convention to determine the 1-4 interactions as well when performing a 
periodic simulation?  From what I see from my visualization, the atoms 
and distances reported in the error are taken from the periodic image.  
Hence while let's say that atom 1 and 4 are within the allowed distance 
in itself, the distance between atom 1 and the periodic image of atom 4 
would exceed the table size.  Not sure if I manage to explain it 
clearly, but i appreciate any help.  Thanks!

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