[gmx-users] Carbon Nanotube Unstable with LJ

David spoel at xray.bmc.uu.se
Tue Aug 9 17:07:45 CEST 2005

On Tue, 2005-08-09 at 09:53 -0400, Bob Johnson wrote:
> Hello everyone,
> I am simulating an infinite nanotube. The force field for the bonds, angles, and
> dihedrals seems to produce a stable tube. However, when I include the LJ
> interactions the tube forms kinks and relaxes into a different structure. I've
> tried getting the LJ pairs from the pair list in the topology file as well as
> from the Generate Pairs option. Although, I'm not 100% sure what the Generate
> Pairs option does. In both cases I'm setting nrexcl to 3. I figured that the
> Generate Pairs option creates LJ pairs for atoms that are separated by 3 (the
> nrexcl setting) bonds. What does the FudgeLJ feature do and when would you want
> to use it?
gen pairs creates parameters that have scaled LJ values. It does not
create interactions. You may want to take the whole pairs section out of
your topol, and increase the nrexcl to 4 or 5.

Did you use pbc=full ?
> My topology was generated in x2top and it seems that the periodic boundary
> conditions are set correctly. The LJ parameters are the following:
> c6 = 5.7353e-3
> c12 = 1.8707e-5
> Thanks,
> Bob Johnson
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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://xray.bmc.uu.se/~spoel

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