VMD-L Mailing List

From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Mon Nov 29 2021 - 03:11:57 CST

Hi Shabir,

Can you please elaborate your problem. I have used CNTs in MD but could not understand what you are trying to ask except that the coordinates do not match. What for do you need "exact" coordinates?

Regards,
Raman

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________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Axel Kohlmeyer <akohlmey_at_gmail.com>
Sent: Sunday, November 28, 2021 1:33:46 AM
To: Kibria Imtiaz Shabbir <shabbir1627046_at_stud.kuet.ac.bd>
Cc: Vmd l <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Re: CNT structure formation

When you don't get a response on a mailing list this has usually one (or multiple) of the following reasons (there are more, but they are less likely).

- people don't understand what you have been asking, either because you have not explained it well enough or because they got confused about your use of the english language
- nobody knows how to answer to request (at least nobody that is subscribed to the mailing list)
- people think that you could easily resolve you problem on your own, e.g. by checking the documentation more thoroughly
- you are trying to do something that cannot be done or makes no sense

None of these issues get resolved with "Kindly tell me the procedure"

On Fri, Nov 26, 2021 at 11:23 PM Kibria Imtiaz Shabbir <shabbir1627046_at_stud.kuet.ac.bd<mailto:shabbir1627046_at_stud.kuet.ac.bd>> wrote:
Dear VMD users,
Kindly tell me the procedure.

Sincerely,

Kibria Imtiaz Shabbir

Undergrad student

Department of Materials Science and Engineering

Khulna University of Engineering and Technology(KUET)

Khulna-9203, Bangladesh

Kibria Imtiaz Shabbir | LinkedIn<https://urldefense.com/v3/__https://www.linkedin.com/in/kibria-imtiaz-shabbir-a33708145/__;!!DZ3fjg!rI_l6pDek5W1v0rg9QgfQOon9HJuIjcdsXROBzd4WW36kfGex1ZMg9PSWo_zDyTw3A$>

On Thu, Nov 25, 2021 at 3:52 PM Kibria Imtiaz Shabbir <shabbir1627046_at_stud.kuet.ac.bd<mailto:shabbir1627046_at_stud.kuet.ac.bd>> wrote:
Dear Altruists,
How can I construct exact same coordination of atoms box in the CNT data file which is developed by VMD?
lattice_box = (80.5*80.5*161) angstrom
Chirality(n,m) = (10,10)
Diameter= 1.3751 nm
length = 7.8566 nm

 # generated by VMD

        1280 atoms
           1 atom types

      0.000000000000 80.5000000 xlo xhi (?????)
      0.000000000000 80.5000000 ylo yhi (?????)
      0.000000000000 161.000000 zlo zhi (?????)

Masses

            1 12.01100000 # C

Atoms # atomic
         1 1 47.125494 40.250000 41.217088
         2 1 46.975248 41.679496 41.217088
         3 1 45.812391 44.291314 41.217088

I got the data.

 # generated by VMD

        1280 atoms
           1 atom types

      0.000000000000 15.559482000000 xlo xhi
      0.000000000000 15.559482000000 ylo yhi
      0.000000000000 79.365517000000 zlo zhi

Masses

            1 12.01100000 # C

Atoms # atomic

         1 1 6.779741000000 0.000000000000 0.000000000000
         2 1 6.631588000000 1.409587000000 0.000000000000
         3 1 6.447917000000 2.095055000000 1.228024000000 (wrong coordination)

Please help me. Your small help will be fruitful for me. 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com>  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!otj66a3WvF3fRyiSgZLSKZFCbyVfbf2cKCdblanMj1N31lGViok4TuPU727dSeDSwg$ <https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!tpeUQEscrben-YpJYM_Cc1ls47WsK6CX5o66AaFRqzOzl9IglKOCNqnvFPCHMKnw2Q$>
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.