OneAngstrom

Alternatively, you can do this without the Brenner interaction model but with the built-in minimization which uses the Universal Force Field (UFF) and the Add editor (shortcut: A) (it's Carbon by default).

First, you will need to modify SAMSON preferences (Ctrl+K):
-1- For the Add editor, disable the "Adjust hydrogens ..." option.

-2- For the Minimization, disable the "Warn me when hydrogens appear to be missing" warning to prevent it from poping-up on each new bond connection.

Then you can apply the minimization: Home >Simulate > Minimize. Start connecting atoms in the nanotube and the graphene sheet using the Add editor (A) - to create a bond simply connect two atoms with this editor.

Dear @Kevin-3 ,

Thank you for posting this question here.

To create such a model you will need to have the Brenner interaction model. It is a paid element, but there is a free trial available and special prices for Academia.

You can check out the SAMSON Tutorials - Essentials 18 - Interactive simulation video that explains how to perform interactive simulations in SAMSON. This video is for an older version of SAMSON, but it should be helpful. To create a model that you attached you would need to create a graphene sheet and then place a nanotube of the desired radius perpendicular to it (you can move, rotate objects using Move editors in SAMSON) and connect them using the same approach as described in the video. So the pipeline would look like this:
-1- Add graphene sheet and nanotube. You can first add a nanotube using the Nanotube creator GUI - this will allow for precise positioning and size - and then placing a graphene sheet. You may also place them using Move editors in the arrangement close to the desired structure. You can use the Viewport compass to rotate the view by precisely 90 degrees and the Zoom to fit to center the model in the viewport (Ctrl+Shift+Space, Shift+Space).

-2- You can remove some atoms from the graphene sheet in the place of the desired connection to facilitate this connection in the following simulation step.

-3- Add a simulator (Ctrl+Shift+M, or Home > Add simulator). Set the Brenner interaction model as an interaction model, set Interaction modeling as a state updater. Increase the state updater's step size to e.g. 0.5 fs.

-4- Start the interactive simulation by clicking Space or Home > Start simulation.

-5- You can select the nanotube in the Document view and move it using Move editors closer to the graphene sheet for bonds to be automatically created between them thanks to the simulator. Else you might need to help to connect them by hand as shown in the video above using Select (shortcut: R) and Move atoms (shortcut: D) editors or Add editor (shortcut: A) (it's Carbon by default).

You can also check the SAMSON User guide - Modeling and Simulation on how to perform simulations in SAMSON.

@aaa Thank you for reporting your solution here!

Hi James, thanks for reporting this. We sent you an email to determine the issue.

Thank you!
This looks like an issue with some integrated graphics cards. We will look into how we can reproduce it and fix it.

Dear @Mizraim,

Could you please check what OpenGL version do you have installed? It should be higher than OpenGL 3.2.

The error message ("atom N not found in buiding block 1ACE while combining tdb and rtp") suggests that, in your model, 1ACE contains a N that should not be there (according to GROMACS topologies). You might have to remove it, or move it to the next residue. You can reorganize atoms, residues, etc. easilyby just dragging nodes around in the Document View.

Hello @Jessica, could you please paste the output of the preparation step in the GROMACS Wizard ?

Hello, could you please tell us which graphics card you have? This seems to indicate a GPU issue.

Indeed in the current version of the Gromacs Wizard, you will need to have a force field which allows for both biomolecules and CNTs. Then you can add such a force field in the settings of the module. However using a 'one-shot parameterization' (e.g. using the ATB server) will not work at the moment with the Gromacs Wizard.