Date: Fri Aug 04 2017 - 01:29:09 CDT

> 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, 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