Re: Creating an infinite graphene sheet

From: jashnvareh 1395 (
Date: Sun May 13 2018 - 11:23:54 CDT

Sorry .. I made a mistake .. its pbwithin and here is the commands I used:
set sel [atomselect top "pbwithin 3 of index 47"]
$sel get index
0 1 44 45 46 47 48 49 92 94 95 961 1007

All the indices obtained are in the primary cell and not in the periodic
I attached a render image (img.tga). The orange is related to the above
indeces.. Then if I connect one to another I get a
long bond like in img2.tga

با احترام
دکتر زینب محمد حسینی
مدیریت آموزشی و پژوهشی مرکز آموزش عالی کاشمر

On Sun, May 13, 2018 at 8:23 PM, Giacomo Fiorin <>

> Obviously for each atom you should exclude the atom itself from the
> selection. Also, you should set the periodic boundary conditions correctly
> for VMD. Why don't you experiment first with a linear polymer, and do the
> more time-consuming 2D graphene sheet later?
> On Sun, May 13, 2018 at 11:34 AM, jashnvareh 1395 <
>> wrote:
>> Thanks a lot for the reply. Maybe I'm wrong but when I try for example
>> "pbwithin 3 of my edge selection" it gave me the indices within the same
>> sheet and not in it's periodic images. if I add bond for those atoms I
>> get a long bond from one edge to the opposite edge of the primary sheet.--000000000000a76a72056c18cb78--

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