[gmx-users] Infinite CNT

David van der Spoel spoel at xray.bmc.uu.se
Tue Apr 24 10:06:25 CEST 2007

Daniel Cheong wrote:
> 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 
> appreciated.
> Thanks!
Did you regenerate the topology after extending the CNT?

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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