[gmx-users] Carbon Nanotube Simulation Issues

Yang Ye leafyoung at yahoo.com
Wed Jul 25 05:29:20 CEST 2007


Sorry that most of us on the list were too busy to read one full page of 
details and download individual files. We might just prefer to download 
one package, and run a script file for us quickly dive into the problem.

Is include in mdout_test.mdp a standard option? Where did you get it? I 
changed it to

include = IffG43b1.n2t

It works. Otherwise, cpp terminates before it generates a full top. 
grompp -pp is always a good friend for grompp error (and thorough 
reading of chapter 5 of manual).

Next issue comes the format of ffG43b1.n2t. I don't think it conforms to 
any GROMACS topology format. Again where does it comes from?

My grompp command line:
grompp_s -f mdout_test.mdp -c SWNT_6_6_144_b4em.gro -p 
SWNT_6_6_144_post_genbox.top -maxwarn 10000000 -pp

It gives a pass, at least.

Hope you can work further on.

Yang Ye

On 7/25/2007 2:41 AM, Christopher Stiles wrote:
> I am trying to simulate a single wall carbon nanotube in a box 
> solvated in water, at 300k for about 200ps. Also once I accomplish 
> this I wish to fix either one end of the tube or fix the center of 
> mass position, although this part is unimportant if I can not get the 
> thing to run at all yet.
> I have created a page with a full detailed account of what I have done 
> and tried so far. http://cs86.com/CNSE/SWNT.htm
> Please note all files where created with Vim in the unix environment 
> so I think I have eliminated the formatting issues.
> Also that I have tried the simulation with many different sized tubes 
> from TubeGen (http://turin.nss.udel.edu/research/tubegenonline.html ), 
> both with and without hydrogen capped ends (this is something I have 
> read in the archives as a possible solution, it makes no difference in 
> the end).
> I have come to the conclusion through the help of many of you that the 
> *.pdb file from TubeGen and mainly the residue “UNK” among other 
> things. If any one has had luck with using a TubeGen file to create a 
> simulation please let me know as to how. Other wise I am looking at a 
> few new options basically all of them involve writing my own files.
> I guess I am looking for advice where to go from here.
> ~Christopher Stiles 
> College of Nanoscale Science and Engineering (CNSE)
> State University of New York, Albany, New York 12203, USA
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