[gmx-users] force field for boron-nitride nanotube
Justin A. Lemkul
jalemkul at vt.edu
Mon Sep 8 12:28:48 CEST 2008
jj beh wrote:
> Dear all user
>
> How can I have a force field for simulation of boron-nitride nanotube?
Has anything like that ever been simulated? If it hasn't, there may not be
paramteers for such a species. I don't believe boron exists as an atom type in
any of the force fields provided by Gromacs.
If all of the above is true, you will have the (very hard) task of deriving new
parameters for your nanotube.
-Justin
> The pdb file of nanotube is as follow:
> HETATM 1 N1 UNK 1 1.597 0.000 -5.015 1.00
> 0.00 N
> HETATM 2 N2 UNK 1 1.129 1.129 -2.870 1.00
> 0.00 N
> HETATM 3 B3 UNK 1 1.129 1.129 -4.291 1.00
> 0.00 B
> HETATM 4 N4 UNK 1 0.000 1.597 -5.015 1.00
> 0.00 N
> HETATM 5 N5 UNK 1 -1.129 1.129 -2.870 1.00
> 0.00 N
> HETATM 6 B6 UNK 1 -1.129 1.129 -4.291 1.00
> 0.00 B
> HETATM 7 N7 UNK 1 -1.597 0.000 -5.015 1.00
> 0.00 N
> HETATM 8 N8 UNK 1 -1.129 -1.129 -2.870 1.00
> 0.00 N
> HETATM 9 B9 UNK 1 -1.129 -1.129 -4.291 1.00
> 0.00 B
> HETATM 10 N10 UNK 1 0.000 -1.597 -5.015 1.00
> 0.00 N
> HETATM 11 N11 UNK 1 1.129 -1.129 -2.870 1.00
> 0.00 N
> HETATM 12 B12 UNK 1 1.129 -1.129 -4.291 1.00
> 0.00 B
> HETATM 13 N13 UNK 1 1.597 0.000 -0.724 1.00
> 0.00 N
> HETATM 14 B14 UNK 1 1.597 0.000 -2.145 1.00
> 0.00 B
> HETATM 15 N15 UNK 1 1.129 1.129 1.421 1.00
> 0.00 N
> HETATM 16 B16 UNK 1 1.129 1.129 0.000 1.00
> 0.00 B
> HETATM 17 N17 UNK 1 0.000 1.597 -0.724 1.00
> 0.00 N
> HETATM 18 B18 UNK 1 0.000 1.597 -2.145 1.00
> 0.00 B
> HETATM 19 N19 UNK 1 -1.129 1.129 1.421 1.00
> 0.00 N
> HETATM 20 B20 UNK 1 -1.129 1.129 0.000 1.00
> 0.00 B
> HETATM 21 N21 UNK 1 -1.597 0.000 -0.724 1.00
> 0.00 N
> HETATM 22 B22 UNK 1 -1.597 0.000 -2.145 1.00
> 0.00 B
> HETATM 23 N23 UNK 1 -1.129 -1.129 1.421 1.00
> 0.00 N
> HETATM 24 B24 UNK 1 -1.129 -1.129 0.000 1.00
> 0.00 B
> HETATM 25 N25 UNK 1 0.000 -1.597 -0.724 1.00
> 0.00 N
> HETATM 26 B26 UNK 1 0.000 -1.597 -2.145 1.00
> 0.00 B
> HETATM 27 N27 UNK 1 1.129 -1.129 1.421 1.00
> 0.00 N
> HETATM 28 B28 UNK 1 1.129 -1.129 0.000 1.00
> 0.00 B
> HETATM 29 N29 UNK 1 1.597 0.000 3.566 1.00
> 0.00 N
> HETATM 30 B30 UNK 1 1.597 0.000 2.145 1.00
> 0.00 B
> HETATM 31 B31 UNK 1 1.129 1.129 4.291 1.00
> 0.00 B
> HETATM 32 N32 UNK 1 0.000 1.597 3.566 1.00
> 0.00 N
> HETATM 33 B33 UNK 1 0.000 1.597 2.145 1.00
> 0.00 B
> HETATM 34 B34 UNK 1 -1.129 1.129 4.291 1.00
> 0.00 B
> HETATM 35 N35 UNK 1 -1.597 0.000 3.566 1.00
> 0.00 N
> HETATM 36 B36 UNK 1 -1.597 0.000 2.145 1.00
> 0.00 B
> HETATM 37 B37 UNK 1 -1.129 -1.129 4.291 1.00
> 0.00 B
> HETATM 38 N38 UNK 1 0.000 -1.597 3.566 1.00
> 0.00 N
> HETATM 39 B39 UNK 1 0.000 -1.597 2.145 1.00
> 0.00 B
> HETATM 40 B40 UNK 1 1.129 -1.129 4.291 1.00
> 0.00 B
> HETATM 41 H41 UNK 1 -2.140 0.000 -5.855 1.00
> 0.00 H
> HETATM 42 H42 UNK 1 0.000 2.140 -5.855 1.00
> 0.00 H
> HETATM 43 H43 UNK 1 2.140 0.000 -5.855 1.00
> 0.00 H
> HETATM 44 H44 UNK 1 0.000 -2.140 -5.855 1.00
> 0.00 H
> HETATM 45 H45 UNK 1 1.582 1.582 5.282 1.00
> 0.00 H
> HETATM 46 H46 UNK 1 1.582 -1.582 5.282 1.00
> 0.00 H
> HETATM 47 H47 UNK 1 -1.582 1.582 5.282 1.00
> 0.00 H
> HETATM 48 H48 UNK 1 -1.582 -1.582 5.282 1.00
> 0.00 H
>
> regards
>
> Javad
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
More information about the gromacs.org_gmx-users
mailing list