From: Albers, Thomas (
Date: Sun Aug 06 2017 - 12:26:58 CDT

I think it was Kernighan who likened floating point numbers to like
piles of sand - every time you move them you lose a little sand and gain
a little dirt.


On 8/6/2017 10:51 AM, vmd-l digest wrote:
> This is an external email. Use caution responding, opening attachments and following links.
> vmd-l digest Sunday, August 6 2017 Volume 01 : Number 3546
> In this issue:
> Re: vmd-l: Molecule builder for large number of molecules
> vmd-l: autoionize not neutralizing the system
> ----------------------------------------------------------------------
> Date: Fri, 4 Aug 2017 17:05:29 +0000
> From: "Vermaas, Joshua" <>
> Subject: Re: vmd-l: Molecule builder for large number of molecules
> 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, 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, 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.
> ------------------------------
> Date: Sun, 6 Aug 2017 20:21:29 +0530
> From:
> Subject: vmd-l: autoionize not neutralizing the system
> Dear vmd users,
> I have a protein solvated in a water box whose net charge is
> 7.999999954365194, so when i am using autoionize to neutralize my system
> it is showing a charge of -4.563480615615845e-8, i also tried to add 8
> chlorine ions instead of going for neutralize option (anyway its more or
> less the same thing), so please kindly help me with this problem.
> regards
> shivam
> ------------------------------
> End of vmd-l digest V1 #3546
> ****************************