Thanks for sharing, Tom!

Hi,

Did you perform other steps (preparation, minimization, equilibration) in GROMACS Wizard before running the production MD (see GROMACS Wizard tutorials)? If not, you might want to try to run them starting from the preparation step.

Could you share the input (all the input files for the step) and resulting files (the corresponding folder into which GROMACS Wizard saved the resulting files, named with a time stamp, e.g. "2024-10-23_09h55m26s-simulate-error") with us so we can try to reproduce the issue and see is the problem?

You don't need to upgrade your whole system; you can try to update it via the above-given commands which will update the packages installed on your system. And if glibc 2.33 is not available with the update you can try to install it from OpenSUSE Tumbleweed.

thank you

Dear @Luis ,

Great! Thanks for checking and for reporting the issue in the first place!

Possibly, it is not supported with Cycles kernels (from Blender's Cycles) that we ship. We will try to see what we can do here. Or, maybe, the Cycles kernels we ship are not compatible with the CUDA version installed on your OS.

Dear @SHANLY ,

You can find the description of the UFF and IM-UFF used in SAMSON in the following papers:
UFF: https://doi.org/10.1002/jcc.24309
IM-UFF: https://doi.org/10.1016/j.jmgm.2017.08.023

And you can find information on how to perform simulations in SAMSON using the integrated force fields in the User Guide: Modeling and Simulation.

Could you please tell us more about what you would like to achieve?

Dear @Grigorii ,

Yes, currently, Adenita does not serialize/save its visual model when saving into a file. You need to reset it via Adenita.

Currently, there is no public extension in SAMSON that can launch/use LAMMPS. But you can export your system into a LAMMPS Data format and load LAMMPS files (data and trajectories) back in SAMSON.

We plan on adding the support for periodic boundary conditions in one of the future releases of SAMSON. For some systems, you can simulate without PBC or by freezing the boundary atoms to fix them.

You can also combine simulations in SAMSON with e.g. ASE package using Python, see Python scripting: Combining SAMSON simulation with ASE calculators

Dear @David-Adrian ,

Thank you for your feedback! We will consider this for future releases. Where would you like to install it, e.g. on another drive or a USB-stick?

Dear @Mattia-Felice ,

Thank you for the feedback! We will consider this for the next releases of SAMSON.

We will surely add more labeling possibilities in the next release.

As for formats from ab initio packages, SAMSON currently supports only Molden and it loads only the molecular structure from it. But we can add the possibility to load other data from it as well.

Dear Rudy, sorry for the delay. You can simply merge the ligand structure into the receptor structure. Precisely, in the document view, drag the ligand node and drop it onto the receptor node (more generally, you can drag and drop nodes around to reorganize your entries).

Then, when you select the receptor and compute the normal modes, the ligand will be taken into account.

Dear @Serena ,
No, we do not use Open Babel or anything else for that. It is done by the AutoDock Vina Extended module.

Dear @AntiDown ,

Ok. I am glad it works for you now.
Thank you for your reply!

Great! I am glad that it worked!
Do not hesitate to contact us if you have any questions or feedback.

Great! Thanks for letting us know.

Hi Pedro,

We're sorry about the issue.

Could you please try to delete the following folders:

(IMPORTANT: make sure you don't have e.g. personal SAMSON documents in these folders that you might want to preserve.)

C:/Users/[USERNAME]/AppData/Local/OneAngstrom/
C:/Users/[USERNAME]/OneAngstrom/
C:/Users/[USERNAME]/Documents/OneAngstrom/

and try to reinstall SAMSON to see what happens?

Maybe there is a need to specify in your Windows settings that SAMSON should use specifically the NVIDIA GPU ? Please let us know.

Dear @Filipe

Normally it should be rendering double bonds by default, but you can change this setting in Preferences > Rendering > Structural models - check the Render multiple bonds option:
5d539e47-b05e-4872-8cc1-d1d36cb34dc5-image.png

As for the PBT format, currently, SAMSON does not have the PBT format exporter, but you can export in OBJ or glTF formats for use in Blender.

Best,
The SAMSON Team

Great contribution!

Hi @albert ,

There are several options for the colorization of structures or visual models (Ribbons is a visual model) based on chains:

The colorization using color schemes. First, select the Ribbons visual model in the Document view that you would like to colorize. Then: Biology > Colorize > Chain ID or Chain (illustrative) (i.e. in the style of D.S.Goodsell)
aedf2d1e-77e3-42cd-af72-51400ba6f73b-image.png
You can also choose "Custom..." from the list and specify the color palette. The colorization with constant colors per chain. Choose a chain in the Document view. Set the color using Visualization > Colorize.

See more in User guide - Colorizing and User guide - Visualizing.