Yes, it would be useful to have the energy profile along the path. Not only the height of the barrier, but also its width, shape, etc.

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.
0_1600418725406_Preferences-Add-no-adjust-H.png

-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.
0_1600418739623_Preferences-Minimize-no-H-warning.png

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.

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.

Thanks Dear.

Dear @DmitriyMarin
Thank you for your reply!
Yes, that LAMMPS wizard would be wonderful.

Best regards,
Patrik Molnár

Hello,

The issue is that SAMSON was installed as Administor. Can you please try to activate User Access Control (UAC) so that Windows does not install SAMSON as admin? Here's a link about how to do that: https://www.technipages.com/windows-enable-disable-user-account-control-uac

Please set UAC to e.g. "Always notify" (you can set it back to the previous setting afterwards).

0_1586188022427_b58888db-0b85-4f3f-8459-6d51649a09ab-image.png

Then, please restart your computer, and install SAMSON again.

Please let me know how this goes.

Thanks,

Stephane

Thank you so much for helping me. I tried to link exactly Qt5.12.5 (my own version is 5.14.1) so it works now. Again, thank you so much.

Best regards,

Dong.

Dear John,

As Stephane pointed out, Adenita is for now compatible just with SAMSON 0.8.5 or 0.7.0, for Windows and Linux. But there are plans to port it to SAMSON 2020 and Mac, I expect this versions to be available during April this year.

Best regards,

Elisa

Dear @Yair-Augusto, Adenita was just updated and this problem should have been fixed. Please let me know if it persists or you find new ones.

Best regards,

Elisa

It does! Thanks a lot.

Dear @sudhir ,

For the protein-ligand simulation, you can check out the Ligand Path Finder tutorial for Ligand Path Finder Element. You can also check out the Ligand unbinding pathway search tutorial for the free Ligand Unbinding Search Element (available only on SAMSON 0.7.0).

As for saving MD trajectories, you can check out the tutorial on exporting atoms trajectories along paths which uses the Export Along Paths Element. This Element allows you to export trajectories into PDB files which you can further analyze using other software.

You can also do some analysis and post-processing in SAMSON thanks to the Python Scripting Element, you can check out the Python Scripting guide for more information, for example, the Computing RMSD sample.

To simulate a protein-membrane complex you can use the GROMACS Wizard Element, using this Element you can easily prepare your system for GROMACS simulation, minimize and equilibrate the structure, and simulate your system using GROMACS. See the GROMACS Wizard tutorial for more information.

Hi,
Actually interactive fitting only VMD is providing and that is also very limited. VMD chops off your actual EM map according to the provided pdb model instead of fitting it into the density.
So, as I want to fit multiple structures in the map, I can not do it. I was trying to fit my multi-chain PDB in the same map but it failed.

Chimera do not provide interactive fitting and it fits the protein poorly in the map. Therefore, it is hard to get a proper knowledge of the conformation of any of these tools.

Rest tools are more programming centric, making them hard to be used by biologists having limited programming skills like me.

Dear Stephane,
Thanks for the link but I tried this too. I does not work all the time. But as I mentioned in YASARA structure, parameterization is a childs' play. How they do it is secret for me but it is kool.
If there will be something like that in SAMSON too, it will be very easy to run complex simulation affectively.

Sorry, SAMSON needs a 64-bit computer to run.

Dear Stephane,

Yes, we have atoms. The 0.8.0 solution will be the best long-term, as we are dealing with large systems and FPS drop a lot when translating or rotating, but for now I will check the ParticlePositionChanged event.

Thanks!!

Elisa

Hi Andrea, sorry for the delay. Typization is normally performed automatically (this is a benefit of this SAMSON Element, as described in the paper Artemova, S., Jaillet, L., & Redon, S. (2016). Automatic molecular structure perception for the universal force field. Journal of computational chemistry, 37(13), 1191-1205.). The typization functions are there when you know for sure that you would like to use a different typization, but even then you should refer to the original UFF paper to make sure this is what you want.

Hello, could you please contact us by email (please reply to the registration email) so we can see what we can do?

Thanks!

The SAMSON team

Hello @Kava ! Thank you for your interest in SAMSON. As far as we know, no one is currently working on the STL exporter. But this would be a really nice feature. For the efficiency and speed reasons, the Gaussian surface is generated on GPU. Therefore, we don't have direct access to resulting shapes and it won't be that easy to export these shapes. We will see what we can do.

Another possibility is to program the Gaussian surface on CPU yourself and export the resulting shape in the STL file (see Documentation for developers).

Rendering of spheres is fast, it is done on GPU, rendering of disks should not make it much faster. It is the Document view, which makes it slower for bigger systems, but it will be faster in the next SAMSON version.

If you want to see the flat visualization of atoms, you can modify the rendering preferences via changing the lightning preferences in SAMSON (see User guide: Visualizing. Lightning section). Basically, in the SAMSON preferences (Ctrl/Cmd+K) go to Rendering > Lightning: set the light intensity for first and second lights to zero; set the ambient light to 1 and the Fresnel intensity to 0.

Thank you for the suggestion, @Cyril !
Yes, for now, it is possible only with an importer for crystallographic .cif files. There is a possibility to replicate crystals thanks to the Crystal Creator App, but it does not expand them periodically with bond connections. We will see what we can do.