Razvan V. Marinescu issues

Results 4 issues of


                                            Razvan V. Marinescu

Segmentation fault - openMM 7.7 + WESTPA 2.0

I'm running openMM 7.7 using WESTPA 2.0, an enhanced sampler. It basically launches ~420 short segments of openMM simulations and runs them in parallel. After 30 WESTPA iterations (each iteration...

Optimizing the runtime on a system of proteins

Hi everyone, I'm trying to optimize the code for openMM to run as fast as possible on a system of 4 proteins (a dimer of dimers): https://www.rcsb.org/structure/2g33. The system has...

Best way to protonate ligands / small molecules to get them ready for GAFF

What is the best way to protonate a ligand / small molecule? I think I successfully managed to protonate my 58H ligand with **pdb4amber** (using the `--add-hydrogens` option) and I...

OpenMM in FP16 or FP8 floating-point precision

Hi, Has anyone tried OpenMM in floating-point precision lower than FP32? Can one still run simulations in FP16 or FP8? Which operations could be ideally moved to lower precision? Thanks!