[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:
> Hi,
>     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).

> Regards,
> George
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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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