large non-protein molecule qmmm or md preparation

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Dear all,

After crawling a few articles, a particular question raised in my mind.

If running md or qmmm, a molecule previously undefined should be redefined under the procedures states in this article:

For example, on the article it gives N3O3. However, if the molecule is large, suppose something like graphene sheet or carbon nanotube, shall the user define the molecule into fragments?

The ATOM definition in pdb file from column 13-16 is atom name. Apparently this four character space is not for defining very large piece of fragments; therefore, I assume molecules like graphene would have to be defined into many small pieces, in order for the atom numbers to be unique. The way to treat this might be constructing building blocks of graphene, and treating the marginal atoms as different residual groups.

Could someone point out any previous examples in this approach, or in case if I am going in a wrong direction, tell me I am wrong, please?


Edited On 5:06:01 AM PST - Thu, Nov 29th 2012 by Sacch

  • Huub Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Hi Alvyn,
In the PDB files from the protein databank the data in columns 13:16 specifies sort of atom type data. These labels do not have to be unique as far as I can see. So I don't think there is a problem at all.
Best wishes, Huub

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Hi Huub,

Thanks for your info.

What I want to say is the point here: " 3. make unique atom names:
This has to do with the requirement that all atoms names have to be unique within a given residue."

My question is that within a single residue the atom names have to be unique. Therefore it seems to be logic to dismentle big molecules like graphene sheet into small identical residues instead of a big piece as a big residue. Am I right?



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