From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Sun May 13 2018 - 13:58:05 CDT
Yeah, VMD doesn't have a clean way of visualizing bonds across periodic images. Basically all VMD knows how to do is to link together atoms *within* a periodic unit cell. Since atoms on the left and right edges should be "bonded", the result is bonds that stretch across the periodic unit cell. When simulated, the pbc is correctly taken into account, and they'll act like short bonds. So basically this looks perfectly normal to me. When visualizing cellulose, I'll often switch to VDW just so it doesn't look dumb.
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: Mon Dec 31 2018 - 23:21:06 CST
-Josh
On 2018-05-13 10:24:00-06:00 jashnvareh 1395 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<mailto: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<mailto: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..
May you guide me on that?
با احترام
دکتر زینب محمد حسینی
مدیریت آموزشی و پژوهشی مرکز آموزش عالی کاشمر
On Sun, May 13, 2018 at 7:38 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com<mailto:giacomo.fiorin_at_gmail.com>> wrote:
For the edge of the nearest periodic image, I suggested you to use an atom selection based on "pbwithin" for each of the edge atoms.
Giacomo
On Sun, May 13, 2018 at 3:11 AM, jashnvareh 1395 <jashnvareh1395_at_gmail.com<mailto:jashnvareh1395_at_gmail.com>> wrote:
Thanks a lot for your prompt answers,
Hi Giacomo,
My question is that in the "topo addbond" command which atom id should be selected for the periodic image?
I have the atom id of my real sheet at the edges but how about the atom id for the periodic image?!
All the Best,
Zeynab
با احترام
دکتر زینب محمد حسینی
مدیریت آموزشی و پژوهشی مرکز آموزش عالی کاشمر
On Sun, May 13, 2018 at 1:57 AM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>> wrote:
Yes. This how we do things like make infinite cellulose, although we have the benefit of specific patches to make the chemistry we are interested in. The most annoying part is making sure that you don't inadvertently introduce a defect at the boundary of the periodic cell. For graphene, this means making sure that your original sheet matches nicely at the edges.
-Josh
On 2018-05-12 12:25:04-06:00 owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> wrote:
Hi, you could try using TopoTools to add bonds between atoms at the edges of the sheet. You could select them automatically, or using spatial criteria. To find the nearest neighbor of each edge atom, a selection based on "pbwithin" should help.
Giacomo
On Sat, May 12, 2018 at 11:34 AM, jashnvareh 1395 <jashnvareh1395_at_gmail.com<mailto:jashnvareh1395_at_gmail.com>> wrote:
Dear all,
I want to run the simulation of an infinite graphene sheet solvated in water.
I don't know how to create an infinite sheet with it's periodic images.
Should I add bonds between graphene and it's periodic images or is not needed?
I searched within the forum but couldn't find a clear answer.
Would be so much thankful to help me..
All the Best,
Zeynab
--
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin
--
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin
--
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin