[gmx-users] CNT Potassium doping with GROMACS
David van der Spoel
spoel at xray.bmc.uu.se
Sun May 13 07:50:50 CEST 2007
George Abadir wrote:
> I want to make a simulation of CNT in an environment of potassium
> atoms to see how they will be adsorbed on the CNT surface (this is a way
> of doping carbon nanotubes). I built a .pdb file with a CNT and some
> potassium atoms with random coordinates around the nanotube. When I run
> x2top to have my topology file, I get the error:"No forcefield type for
> atom K with 0 bond". The problem is that the atoms of potassium should
> indeed be not bonded to anything at the beginning of the simulation.
> Does anybody have a way to describe such a system and avoid this error?
> Thank you very much in advance,
first make a topology for the CNT with x2top, then manually add the
potassium (chapter 5).
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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://folding.bmc.uu.se
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