[gmx-users] Infinite CNT

[David van der Spoel]

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.
________________________________________________________________________
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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