README_VMD_graphene.txt
4a1807d39739efficient_neuronet

README_VMD_graphene.txt
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			------- A note on building the graphene sheet in VMD: ------

			Probably you can ignore these instructions.
			These instructions are not necessary for this example to run.

			This example contains several pyramid shaped objects resting on a surface
			made of graphene. The instructions in this file explain how to build the
			graphene (representing the "ground") using VMD instead of with moltemplate.
			Why do this?
			VMD can create graphene sheets with bonds connecting neighboring carbon atoms,
			(which looks more pretty). However, as of 2013-4-29, moltemplate currently
			can not generate these bonds. It does not matter physically in this case,
			because the graphene sheet used here does not move. It is only used as
			scenery, to graphically represent the ground surface.

			Select "Extensions"->"Modeling"->"Carbon Nanotube Builder"
			Build a graphene sheet of size 39.8 x 39.8 (units: nm)
			400.3358398 399.876008
			(try to use a size compatible with the periodic boundaries)
			Select "Extensions"->"Tk Console", and type
			display backgroundgradient on

			Note: If you want to do this, before you run moltemplate, you may want to delete
			the sections of the "system.lt" file (located in "moltemplate_files")
			which define the graphene wall. Instead create the graphene data file
			in VMD. You will have to manually merge the data file for graphene
			with the data file for the pyramids created by moltemplate,
			(taking care to avoid overlapping atom-id numbers).