lohedges
commented
10 months ago Thanks for reporting.
I can reproduce the first issue. It looks like someone has incorrectly put a try_import block inside our metadynamics helper script. (This is a patched version of the OpenMM metadynamics driver). This means that the code is no longer self-contained and can be run without BioSImSpace.
Just trying to reproduce the second problem.
Hi,
I have been working witht he tutorials, and reproducing them in my system. Recently I found an issue on the funnel methadynamics tutorial. This happens only in the part were the methadynamics run with OpenMM:
protocol = BSS.Protocol.Equilibration(runtime=0.01*BSS.Units.Time.nanosecond) process = BSS.Process.OpenMM(minimised, protocol)
Start the process in the background.
process.start()
Wait for the process to finish.
process.wait()
*First I got a problem importing ..._utils on the methadynamics.py script
Traceback (most recent call last): File "/cluster/ddu/cmmartinez001/Projects/openB/fun-metaD-work_dir/openmm_script.py", line 6, in
from metadynamics import *
File "/cluster/ddu/cmmartinez001/Projects/openB/fun-metaD-work_dir/metadynamics.py", line 31, in
from ..._Utils import _try_import
ImportError: attempted relative import with no known parent package
*Then instead of calling openMM like that I changed it for :
import openmm as mm import openmm.unit as unit
*Then error I got is this:
Traceback (most recent call last): File "/cluster/ddu/cmmartinez001/Projects/openB/test/openmm_script.py", line 111, in
simulation = Simulation(prm.topology,
File "/cluster/ddu/cmmartinez001/miniconda3/envs/CST/lib/python3.9/site-packages/openmm/app/simulation.py", line 103, in init
self.context = mm.Context(self.system, self.integrator, platform, platformProperties)
File "/cluster/ddu/cmmartinez001/miniconda3/envs/CST/lib/python3.9/site-packages/openmm/openmm.py", line 2694, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Two Forces define different default values for the parameter 'k'.
*I got those errors even in the example.
Just wondering if I am doing something wrong. I prepare a folder where I have the inputs and followed the tutorial described.
Biopsimspace version: 2023.5.0.dev+35.g66512f27 Python 3.9
Thanks a lot,
Cesar