insukjoung

Hi, I have the same problem. (version 2021.4-plumed-2.7.3) CUDA 11.2 mpich 3.4.3 GPU: Tesla V100 After writing the checkpoint file, it hangs. Once it happens, the generated cpt file will...

I use parmed to generate the topology. By default parmed does not generate `position_restraints` in the topology file for both ligand and protein systems. Currently, there is no `position_restraints` in...

I found other related issues. For pre-solvated systems, `gmx genion` must be run to neutralize the complex system. Currently, this step is skipped if the system is pre-solvated. When the...

Here is another related problem. The topology file generated in the `protein` leg. The order of `LIG` is misplaced like: ``` [ molecules ] ; Compound #mols LIG 1 system1...

> Here is another related problem. > > The topology file generated in the `protein` leg. The order of `LIG` is misplaced like: > > ``` > [ molecules ]...

> Yes, that's a current limitation of the prepare_dual_topology.py. I hope I can remove that eventually, but I am not sure how exactly. May be the LIG line could be...

> ```python > from openff.toolkit.utils import toolkit_registry_manager, AmberToolsToolkitWrapper, RDKitToolkitWrapper, ToolkitRegistry > with toolkit_registry_manager(ToolkitRegistry([AmberToolsToolkitWrapper(), RDKitToolkitWrapper()])): > ligand_system = force_field.create_openmm_system(off_topology) > ``` > > Could you let me know if that works?...

On behalf of my colleague, #1896