[gmx-users] errors on carbon nanotube

David van der Spoel spoel at xray.bmc.uu.se
Sat Jun 24 11:00:20 CEST 2006

jackyxh at 163.com wrote:
> Hi,GMX group and other users:
> I am a gromacs(version 3.3) user. I want to do carbon nanotube(CNT) MD.
> Months ago, when I ran grompp, she told me that something was wrong.
> (see http://www.gromacs.org/pipermail/gmx-users/2006-April/021092.html)
> After i got suggestions from GMX group and other users (really thank Bob
> who has given me some importent advices!) and checked almost
> all of the "Mailing lists" about CNT, i began other ways to generate
> my files (.gro .top and so on).
> This morning i got the results of my working----ERRORS!
> So I type this for help AGAIN.
> I will tell what I have done in details, may anyone could give me a hand.
> <What i have?>
> a "cnt.pdb" and a "cnt.gro" which i write by myself on the base of "cnt.pdb"
You can generate a gro file from pdb by editconf but you don't need it 
for this.

The easiest way to get a topology is to use x2top. The errors you showed 
are probably due to periodic boundary conditions.
Is your nanotube supposed to be infinitely long? In that case, is the 
box size in the pdb file correct?
If it is not supposed to be infinite you need to cap the ends with 
hydrogen atoms or something like that.

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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