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smog-server / OpenSMOG

OpenSMOG is a Python library for performing molecular dynamics simulations using Structure-Based Models. OpenSMOG uses OpenMM.
MIT License
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more cryptic messages #37

Closed Whitford closed 2 years ago

Whitford commented 3 years ago

sbm_CA3.createReporters(trajectory=True, energies=True, energy_components=False, interval=1) Traceback (most recent call last): File "", line 1, in File "/Users/whitford/miniconda3/envs/openSMOG/lib/python3.9/site-packages/OpenSMOG/OpenSMOG.py", line 378, in createReporters self.simulation.reporters.append(DCDReporter(dcdfile, interval)) AttributeError: 'SBM' object has no attribute 'simulation' sbm_CA3.createSimulation() Traceback (most recent call last): File "", line 1, in File "/Users/whitford/miniconda3/envs/openSMOG/lib/python3.9/site-packages/OpenSMOG/OpenSMOG.py", line 336, in createSimulation self.simulation = Simulation(self.Top.topology, self.system, self.integrator, self.platform, self.properties) AttributeError: 'SBM' object has no attribute 'Top' sbm_CA3.loadSystem(Grofile=sbm_CA_grofile, Topfile=sbm_CA_topfile, Xmlfile=sbm_CA_xmlfile)creating force contact_gaussian from xml file Files loaded in the system.

Whitford commented 2 years ago

Vinicius, is this still an issue? From the original posting, I'm not even sure how to reproduce this. I think we probably put in some checks that will prevent anyone from hitting it. If you like, go ahead and close this issue.

junioreif commented 2 years ago

this type of issue arises when the system isn't initialized (by setup_openmm()) now we have a check function to warn if it happens