From: jashnvareh 1395 (jashnvareh1395_at_gmail.com)
Date: Wed May 16 2018 - 00:54:03 CDT
Hi Josh,
Yes it's exactly what you said. Thank you so much to making the things
clear..
In my case I did exactly the same as what you said. using "topo addbond"
command I made the connections between primary cell and it's images. I did
the preparation protocol (minimization and heating up the system). Within
this procedure everything is OK and the connections are kept in the way
that I have an infinite sheet. I then do the NPT simulation to make sure
about the uniform density of the water molecules.
This step destroyed the the bonds between primary cell and it's images. I
even tried fixing the carbons and doing NPT but finally only the waters
shrink and if I then do normal NVT for the data collections I ends up
with a non-uniform water box again. Any suggestion on that?
با احترام
دکتر زینب محمد حسینی
مدیریت آموزشی و پژوهشی مرکز آموزش عالی کاشمر
On Sun, May 13, 2018 at 11:28 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:
> 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.
>
> -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>
> 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.
>>> 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> 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> 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> 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 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> 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://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgoo.gl%2FQ3TBQU&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C9aeb02ac3f194ab68a6608d5b835ac36%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636617463035631609&sdata=y%2BjikkoGuqDMiQkZxpeGi5OtCckmgjmT2PbYEoZbLpk%3D&reserved=0>
>>>>>> https://github.com/giacomofiorin
>>>>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fgiacomofiorin&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C9aeb02ac3f194ab68a6608d5b835ac36%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636617463035641614&sdata=jNz87wupVjyfyQmhBaqfv7OuRrEXXj3vGAUDOa4ZEPs%3D&reserved=0>
>>>>>>
>>>>>>
>>>>
>>>>
>>>> --
>>>> Giacomo Fiorin
>>>> Associate Professor of Research, Temple University, Philadelphia, PA
>>>> Contractor, National Institutes of Health, Bethesda, MD
>>>> http://goo.gl/Q3TBQU
>>>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgoo.gl%2FQ3TBQU&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C035a80490c8b44d43c5308d5b8edecbe%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C1%7C636618254403833048&sdata=tycv5uHiWD1MNN9Zc6qyHzJcUygwBJqBdYYrarKf4o8%3D&reserved=0>
>>>> https://github.com/giacomofiorin
>>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fgiacomofiorin&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C035a80490c8b44d43c5308d5b8edecbe%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C1%7C636618254403833048&sdata=ycWkeCzNhYUi3aHSAl2IHLd0rnGj702wkLPhgl%2Fc120%3D&reserved=0>
>>>>
>>>
>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Contractor, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgoo.gl%2FQ3TBQU&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C035a80490c8b44d43c5308d5b8edecbe%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C1%7C636618254403833048&sdata=tycv5uHiWD1MNN9Zc6qyHzJcUygwBJqBdYYrarKf4o8%3D&reserved=0>
>> https://github.com/giacomofiorin
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fgiacomofiorin&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C035a80490c8b44d43c5308d5b8edecbe%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C1%7C636618254403833048&sdata=ycWkeCzNhYUi3aHSAl2IHLd0rnGj702wkLPhgl%2Fc120%3D&reserved=0>
>>
>
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