Miroslav Suruzhon

Water molecules not recognised as separate molecules

4

Hello, I have found an issue, where I try to load in a system containing a protein and water molecules from AMBER `parm7` and `rst7` [files](https://github.com/michellab/BioSimSpace/files/8676414/Archive.zip). In short, `BioSimSpace` doesn't...

Numerical instability at 4 fs with the LangevinMiddleIntegrator

19

Hello, I have been testing the `LangevinMiddleIntegrator` functionality in Sire by trying to run 4 fs simulations with HMR but I have been running into numerical instabilities both on CPU...

Problem when converting Gro/Top to Rst7

12

Hello, I have run into an issue when trying to load an alchemical system generated by a GROMACS run, squashing it and writing it out as an AMBER rst7 (writing...

Biopython 1.86 PDBs are no longer compatible with RDKit

3

Consider the following simple rountrip of `rdkit` -> pdb -> `biopython` -> pdb -> `rdkit`: ```python from rdkit import Chem from rdkit.Chem import AllChem from Bio.PDB import PDBParser, PDBIO import...

Minimisation results in much higher energies after OpenMM 8.0.0

4

Hi, I am running the following simple script: ```python import openmm from openmm import app from openmm import unit from openmmtools.testsystems import WaterBox test_system = WaterBox() integrator = openmm.openmm.LangevinMiddleIntegrator(300 *...