VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Aug 04 2017 - 12:05:29 CDT

Hi Shrivam,

My only advice is to break it up into parts. Focus on adding one thing
at a time to your sheet. I have no idea what the builder spits out or
how far along you are in the process, but looking around for resources
on VMD's atomselection logic probably helps. For instance, to pick out
carbons on the edge, you might do something like "name C and numbonds ==
2". Or if you wanted something adjacent to those atoms, try "withinbonds
1 of numbonds == 2". VMD atomselection logic is awesome and powerful,
but the scripting and logical thought is not something we can really do
for you.

Good luck!
-Josh Vermaas

On 08/04/2017 12:29 AM, t.shivam_at_iitg.ernet.in wrote:
>
>> Hi Shivam,
>>
>> Scripting it in VMD would be my solution, but that is my solution to
>> most things, so I might be biased. If you have one copy of your
>> functional group made in Avogadro or Molefacture, you would add it to
>> your sheet in VMD as many times as needed, merge the functional groups
>> to your sheet, and then add bonds and guess angles and dihedrals.
>> Pseudocode for a TCL script would look something like:
>>
>> #Load your graphene
>>
>> for { set i 0 } { $i < $numfunctionalgroups } { incr i } {
>> #Load your functional group
>>
>> #Place your functional group
>> }
>> package require topotools
>> set newmol [::TopoTools::mergemols [molinfo list]]
>>
>> #Add in the bonds between functional groups and the main sheet
>>
>> topo guessangles
>> topo guessdihedrals
>>
>> #Write out your new files.
>>
>> However, before you go filling in the blanks, I'd do a bit of googling
>> first to see how other folks made graphene oxide in their own studies,
>> since you aren't the first to look at making graphene oxide, so there
>> may be tools that exist that I know nothing about.
>>
>> -Josh
>>
>> On 07/31/2017 07:33 AM, t.shivam_at_iitg.ernet.in wrote:
>>> I am trying to create a graphene oxide sheet, for that i have generated
>>> a
>>> graphene sheet using Nanotube builder plugin in vmd and trying to edit
>>> that sheet to add the functional groups,for that I tried to use vmd
>>> molefacture plugin but my sheet is too big for that, i even tried to use
>>> AVOGADRO but even it is hanging for large sheets, so can you suggest any
>>> open source or free molecule editor or any other method that can handle
>>> large number of molecules easily.
>>>
>>> Best regards
>>> Shivam Tiwari
>>>
>>>
>>>
>>>
>>
> Hello Dr. Josh,
>
> Thanks for your suggestions, i will try to implement them, but i want
> explain you my problem in little bit more detail,as you have explained
> that i can use tcl scripting for the purpose, the graphene oxide contains
> 3 functional groups- hydroxyl,epoxy and carboxyl so according to
> literature the widely accepted model for GO is that the carboxyl groups
> occupy the carbon atoms on the edges and the functional group is randomly
> occupying carbon atoms, the hydroxyl and epoxy are attached on the basal
> plane, that too are occupied randomly,the orientation of the functional
> group are also up and down from the basal plane, so how can i bring these
> complexities in the script, as my sheet contains around 3000 carbon atoms
> and also i want to know how vmd creates the graphene sheet, is it similar
> to the pseudo script you have shown above? Lastly i have gone through some
> papers and no where the authors mention how they have created the GO
> sheet.
>
>