@Federico-Maria ,
Great! Thanks for checking!

Thanks for mentioning, the thing in 'About SAMSON' will be fixed with the next patch release of SAMSON.

This is going to be so cool. It will allow me to make parts so much faster, and parts can be made larger than in NE1. Perhaps Z88 would make a good extension to do exciting stuff with meshes inside SAMSON. https://en.wikipedia.org/wiki/Z88_FEM_software

@Jocelyn

Hi,

It's GNOME Shell 48.5

Thanks.

We have posted a brief tutorial on preparing protein-ligand systems with GROMACS Wizard. We will add more information to it over time, specific to each parametrization tool/server.

The groups on the SAMSON Connect website are mainly for collaboration purposes (see: User Guide: Collaboration), but they can be extended to manage licenses.

Dear @Ricardo-2 ,

Due to policy updates, we no longer support older versions of SAMSON and have removed them from access.
Could you please tell us which features are missing for you in the latest SAMSON and which version of SAMSON you want to install?

Dear Michael,
I fixed the issue in the GROMACS importers (trajectories, .gro) on macOS that was causing the options to be disabled and was also affecting the GROMACS Wizard. Could you please check whether the GROMACS Wizard and loading of GROMACS trajectories now work for you?

Hi @John-4 ,

In the first Python script you showed, the LLM you used (did you use Gemini or SAMSON's AI Assistant?) hallucinated and used some non-existent libraries, classes, and functions in SAMSON, which resulted in errors.

Ok, got it. SAMSON is a high priority application, so on C: it goes.

Dear @Dominic ,

We've just updated the Adenita extension: it now sets the nucleotide names as expected by PDB - DA, DC, DG, DT. Now, it should be suitable for export in the PDB format.

Hi @Nicolo-0 ,
No, currently, there is no option to specify that H-bonds in an H-bond group (which is part of a structural model) should be displayed between hydrogens and acceptors - they are drawn between donors and acceptors, since hydrogens might be implicit. However, we can add such an option in the next major release of SAMSON.
But if you want it just for the sake of visualization, then you can try setting hydrogens as donors programatically (via Python). Note that this should be done without calling update() since this will recompute the bonds.

To update the topic and for information:
If you are looking for instructions on how to create Python bindings for your SAMSON Extension, please refer to the Developer Guide: Creation of Python Bindings for SAMSON Extensions.

Great video, Tom! Thanks for posting it!

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?