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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