Anton Siomchen

I noticed, that when molplotly used with dash>=2.10 is used then deprecation warning is raised and also plot are duplicated (as mentioned in #31 Replacement of the `JupyterDash` with `Dash`...

Fixing ligand connectivity on the fly

1

I'm trying to calculate ligand-aminoacid interaction from OpenMM simulation from pdb topology and xtc trajectory. Ligand structure is show below  But due to the use of pdb, MDAnalysis makes...

Better way to save structure

1

I'm using OpenMM to build and simulate a protein-ligand system constructed from protein PDB and ligand SDF files. The results are saved as minimised solvated structure in PDB file and...

Reset simulation step counter

1

I'm running simulations in stages: NVT --> NPT --> Production Is it possible to somehow reset the simulation step counter to 0, instead of continuing from the last step from...