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pablo-arantes / making-it-rain

Cloud-based molecular simulations for everyone
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TypeError: Unit "kilojoule/mole" is not compatible with Unit "kilojoule/(nanometer*mole)". #87

Closed sflores14 closed 7 months ago

sflores14 commented 7 months ago

Hello,

Within the Amber.ipynb notebook I ran the "Runs an Equilibration MD simulation (NPT ensemble)" cell block and received the following error:

TypeError: Unit "kilojoule/mole" is not compatible with Unit "kilojoule/(nanometer*mole)".

In the code cell, I changed:

simulation.minimizeEnergy(tolerance=10*kilojoule/mole), maxIterations=int(Minimization_steps))

To:

simulation.minimizeEnergy(tolerance=10kilojoule/(nanometermole), maxIterations=int(Minimization_steps))

And so far the Equilibration is running. I am unsure if the appropriate units should be "kilojoule/(nanometer*2mole)" or "kilojoule/(nanometer*mole)" in this step.

LabPsycho commented 7 months ago

This may not be correct, I just changed line 186 in the Parameters for MD Equilibration From:

simulation.minimizeEnergy(tolerance=10*kilojoule/mole), maxIterations=int(Minimization_steps))

To: OMIT SPACES BEFORE AND AFTER simulation.minimizeEnergy(tolerance=10 kilojoule/(nanometer * mole), maxIterations=int(Minimization_steps))

Now it is running. I wonder if the original notebook has been modified?

pablo-arantes commented 7 months ago

Hi All,

Apologies for the delay, and thank you for bringing the issue to my attention. The latest release of OpenMM (version 8.0) has introduced changes to the nomenclature. I am in the process of updating all the notebooks to ensure compatibility with OpenMM 7.7. This version should resolve the issues we're facing.

@LabPsycho, it appears you've made the correct adjustments.

Thank you.

Best regards,

pablo-arantes commented 7 months ago

Hi All,

I've fixed the code for all the notebooks. Now everything should be working fine. I'm closing this issue.

Thank you

LabPsycho commented 7 months ago

Thank you. And thank you 10X for you and your team's incredible efforts in making make it rain - it has been exceptionally helpful! On Monday, December 4, 2023 at 03:09:43 AM EST, Pablo Ricardo Arantes @.***> wrote:

Hi All,

I've fixed the code for all the notebooks. Now everything should be working fine. I'm closing this issue.

Thank you

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

LabPsycho commented 6 months ago

Hello - I noted a similar error posted about 1 hr ago on GitHub, but the poster did not post the details: When loading dependencies, here is there error. I also note I have this error when trying to run openmm on a local machine. Something with 'import pytraj as pt' ? ModuleNotFoundError Traceback (most recent call last)

in () 1 get_ipython().system('mamba install -c conda-forge ambertools -y') ----> 2 import pytraj as pt 3 get_ipython().system('pip -q install py3Dmol') 4 get_ipython().system('pip install git+https://github.com/pablo-arantes/biopandas') 5 get_ipython().system('mamba install openmm=7.7.0') ModuleNotFoundError: No module named 'pytraj' On Monday, December 4, 2023 at 03:09:43 AM EST, Pablo Ricardo Arantes ***@***.***> wrote: Hi All, I've fixed the code for all the notebooks. Now everything should be working fine. I'm closing this issue. Thank you — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>