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From: Axel Kohlmeyer <akohlmey@...24...>
Date: Sun, 17 Dec 2017 16:45:13 -0500

On Sun, Dec 17, 2017 at 1:17 PM, Γρηγορης Δεδες via lammps-users <> wrote:
Dear users,

I have modeled a cnt through vmd with a molecular atom style(bonds,angles, dihedrals included). 
I am using periodic boundary conditions and a box that is quite larger(10 times) than the dimensions of the cnt in x,y directions and equal to the dimension of cnt in z direction. 

​why so large in x and y? why not using fixed boundaries there?
why so tight in z? ​
During equilibration i use an npt fix 300 300 1 iso 0 0 1 drag 1

​why couple the the box size in x and y to the box size in z and only allow isotropic box changes?
why use fix npt in the first place? ​
I run it for 400000 time steps and although the potential energy equilibrates and the temperature somewhat does the box is expanding 5 times its size and does not stabilize.
I also get a warning : bond/angle/dihedral extent >half of periodic box size.
If you any idea about the cause of the problem or any suggestion regarding its fix please let me know.

​well, do you have one or more bonds with that extreme length?​ e.g. by adding bonds across periodic boundaries.

it is difficult to make any specific suggestions, since you don't provide any specific information, but only rather vague descriptions and no explanations for rather unexpected choices.



Thank you very much,

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Dr. Axel Kohlmeyer  akohlmey@...12...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.