From: Aksimentiev, Aleksei (aksiment_at_illinois.edu)
Date: Sun May 13 2018 - 12:38:52 CDT
Try inorganic builder if VMD
> On May 13, 2018, at 11:28 AM, jashnvareh 1395 <jashnvareh1395_at_gmail.com> wrote:
>
> Sorry .. I made a mistake .. its pbwithin and here is the commands I used:
> set sel [atomselect top "pbwithin 3 of index 47"]
> atomselect4
> $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
> image..
> 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 <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> 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 <
>> jashnvareh1395_at_gmail.com> 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.
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