Error while trying to run the OpenMM simulation

[HadadIdan]

Requested periodic boundary conditions for a Topology that does not specify periodic box dimensions

While trying to run a python file created by the OpenMM script builder, that can be found here: https://github.com/TechnionYP5779/SimuMole/blob/run_simulation_brunch/src/SimuMole/media/files/openmm.py

with the a .pbp file named "bothpdb_16DY4movement_pdb_25ZKHmovement.pdb", that can be found here: https://github.com/TechnionYP5779/SimuMole/blob/run_simulation_brunch/src/SimuMole/media/files/both__pdb_16DY4movement_pdb_25ZKH__movement.pdb

The same happened to me with another 2 molecules (6DY4 twice) Please help.

To run the script simply run "python openmm.py" in a folder with both the script and the pdb file specified above.

[IlanitSmul]

in openmm.py, line 10: system = forcefield.createSystem(pdb.topology, nonbondedMethod=app.PME,

The problem is caused by the nonbondedMethod=app.PME parameter. Try replacing it with nonbondedMethod=app.NoCutoff.

This change fixes the error you specified, but there are still other errors about the rest of the code - so you probably have to check which parameters can be replaced.

[HadadIdan]

Thanks both @IlanitSmul and @MichaelShohat I have found settings that allow for a working simultaion, and they can be seen on https://github.com/TechnionYP5779/SimuMole/tree/run_simulation_brunch . Changing the nonboundedMethod did help as Ilanit suggested, but there were other changed that allowed it to work. We are now using a different, basic openMM script builder.