Razvan V. Marinescu

does anyone have a solution for **writing** an MDAnalysis universe as PDBx/mmCIF?

I just tried `pdb_tocif`, but it screws up the segids. It should have segid of B0, or B1, ... It only keeps the chain (B). See the question marks below:...

A few more details. The 2g33 protein has 4 chains, which I re-packed with PACKMOL, to study how they bind together. The original un-hydrogenated system had a total of 4658...

Thank you very much! That all makes sense. I just tried all that you suggested, and I now get **470ns/day**, which is great! This is equivalent to the GBSA benchmark...

@peastman, thank you!! Your suggestion about the CUDA contexts might be what's happening, as I'm running ~400 threads/processes in parallel (on 4 GPUs only), and I think 10+ processes run...

That makes sense. I think the WESTPA **manager** should be able to do that, I'll look into it.

I'm afraid we don't have those models in higher resolution, but it can be done. Essentially, you need to run a segmentation algorithm on an MRI scan, and then convert...

Alternatively, you can also start right from a template/atlas segmentation .nii file, and convert each mask-id to a cortical surface mesh .ply file

@araikes, actually I think it's possible, cause you can just manually segment *one scan only*. Those segmentations can then be used to create those ply objects for blender. If you,...

@araikes yes, exactly. you only need the segmentation files (don't need the original NIFTI). You just need to break the multi-label segmentation apart into individual segmentations, then convert each of...