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vmdAssist "Build" menu:

You can convert any sheet structure to a nanotube, nanotorus, spiral nanotube, or spiral sheet using vmdAssist. Here is a simple step-by-step instruction on how to make these structures with vmdAssist.

Convert sheet structure to Nanotube:

I) First method:

In this example, we will use the orthogonal unit cell of MoS2, which you can find in the link below:
https://drive.google.com/file/d/19iqs7ERTZ0JWAqdtopxsydK2B5ZZREbk/view?usp=sharing

1. Load MoS2_unitcell.pdb in VMD:
   a) Go to “ File -> New Molecule “ in the VMD Main window.
   b) Click the “Browse” button.
   c) Select MoS2_unicell.pdb from your computer and click on the “Open” button.
   d) Change the file type to PDB from the list and click the “Load” button.
   (You can also drag and drop the file into VMD to load it automatically.)

2. Open vmdAssist from the menu bar, “Externtions -> vmdAssist”

3. Click and select the loaded MoS2_UnitCell.pdb file from the “Molecule list” in the vmdAssist window.

4. From the “Super Cell Builder” tab of the vmdAssist window, enter the desired length of the sheet for x and y directions (e.g., Lx: 50 and Ly: 100). Then click on “Generate” to extend the unit cell and make a sheet. It will add a new molecule.

5. Now select the newly created sheet from the “Molecule list”.

6. To build a nanotube from a sheet:
   a) Go to the “Build” tab of vmdAssist
   b) Select the “Sheet plane” (e.g., xy, because the generated MoS2 sheet in this example is in the xy plane).
   c) Select your desired “Rolling direction” (because in this example, MoS2 is in the xy plane, so we have two options: x or y).
   d) If you need some portion of a nanotube, change the “Arc” value. In this example, leave the “Arc” value at 360 to have a full nanotube.
   e) Click on the “Nanotube” button to make a nanotube from the sheet.

II) Second method:

If you have a prebuilt sheet structure, take the following steps. In this example, we use Graphene_50x100nm.pdb file, which you can download from the link below:
https://drive.google.com/file/d/1tCCcnFeXCDPevi0EzV2gBPCiHooHfCN_/view?usp=sharing

1. Load “Graphene_5x20nm.pdb” in VMD:
   a) Go to “ File -> New Molecule “ in the VMD Main window.
   b) Click the “Browse” button
   c) Select “Graphene_5x20nm.pdb” from your computer and click on the “Open” button.
   d) Change the file type to PDB from the list and click the “Load” button.
   (You can also drag and drop the file into VMD to load it automatically.)

2. Open vmdAssist from the menu bar, “Externtions -> vmdAssist”

3. Click and select the loaded “Graphene_5x20nm.pdb” file from the “Molecule list” in the vmdAssist window.

4. To build a nanotube from a sheet:
   a) Go to the “Build” tab of vmdAssist
   b) Select the “Sheet plane” (e.g., xy, because the graphene sheet for this example is in the xy plane).
   c) Select your desired “Rolling direction” (because in this example, graphene is in the xy plane, we have two options: x or y).
   d) If you need some portion of a nanotube, change the “Arc” value. In this example, leave the “Arc” value at 360 to have a full nanotube.
   e) Click on the “Nanotube” button to make a nanotube from the sheet.

Convert sheet structure to Nanotorus:

To build a nanotorus from a sheet, follow the above instructions for a nanotube, and just in the last step (I.6.e / II.4.e), click on the “Torus” button.

Convert sheet structure to Spiral Nanotube:

Creating a spiral nanotube has the same instructions as creating a nanotube, with some extra settings. For the last step (I.6 / II.4), do the following:
a) Go to the “Build” tab of vmdAssist and find the “Spiral Nanotube” section.
b) Enter the number of rings you need (e.g., 3).
c) Enter the distance between rings in angstrom units (e.g., 10).
d) Click on the “Build” button to convert the sheet to a spiral nanotube.

Convert sheet structure to Spiral Sheet:

Creating a spiral sheet has the same instructions as creating a nanotube, with some extra settings. For the last step (I.6 / II.4), do the following:
a) Go to the “Build” tab of vmdAssist and find the “Spiral Sheet” section.
b) Enter the number of rings you need (e.g., 3).
c) Enter the distance between rings in angstrom units (e.g., 10).
d) Click on the “Build” button to convert the sheet to a spiral sheet.