[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
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