[gmx-users] Unstable Carbon Nanotube

David spoel at xray.bmc.uu.se
Wed Aug 3 08:25:33 CEST 2005

On Tue, 2005-08-02 at 18:19 -0400, Bob Johnson wrote:
> Hello,
> I am currently simulating a single carbon nanotube to verify that I have a
> correct force field. Based on advice found on the GROMACS Mailing List I am
> performing simulations where only bonded interactions are calculated, another
> where bonded and angle interactions are calculated, and so on. Performing the
> simulations with only the bonded interactions still results in a mess: the
> nanotube collapses on itself and becomes this amorphous cylinder. The energy
> and temperature during the simulation are fine. This is a very strange result
> to me. The bonded interactions are as follows:
> Morse Potential
> D = 478.9 kJ/mol
> r_0 = 0.1418 nm
> gamma = 21.867 nm^-1
> It seems that this potential should produce a fairly rigid structure. However,
> that's not what I'm seeing here. Any suggestions?

Watch the movie, if it contracts at the end you have periodicity
problems. Is your topology periodic as well?

> Thanks,
> Bob
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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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