| 5:02:32 AM PST - Thu, Nov 29th 2012 |
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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:
http://nwchemgit.github.io/index.php/QMMM_Appendix#Preparing_QM.2FMM_calculations_from_scrat...
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?
Best,
Alvyn
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