[gmx-users] Carbon Nanotube Simulation Issues

[Christopher Stiles]

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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