[gmx-users] Infinite CNT

David van der Spoel spoel at xray.bmc.uu.se
Tue Apr 24 11:19:17 CEST 2007

Daniel Cheong wrote:
> 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!
did you use pbc = full ?

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

More information about the gromacs.org_gmx-users mailing list