Using OpenMMTools in Google Colab

CondaExampleWithOpenMM.ipynb

Hi Oliver, if they have migrated to Python 3.7, then you should also download the latest Miniconda (instead of v4.5.4). I will test this later this week and update this notebook. Thanks for the report!

Hello Jaime,
Thank you for your reply!
I have tried again using Anaconda2, and it works!

!wget -c https://repo.anaconda.com/archive/Anaconda2-2019.03-Linux-x86_64.sh
!bash ./Anaconda2-2019.03-Linux-x86_64.sh -b -f -p /usr/local
!conda install -y --prefix /usr/local -c omnia/label/cuda100 -c conda-forge openmm
import sys
sys.path.append('/usr/local/lib/python2.7/site-packages/')
import simtk.testInstallation
simtk.testInstallation.main()

Still, it would be really helpful if you could get it work on Python3 (as OpenMM recommended on their website). I haven't seen any error or issue using Python2 yet.

Sorry I forgot to mention that we have to change the runtime type to Python2 and of course with GPU before get started.

Hi Oliver, a year later, I found out what was happening: the conda solver sneakily updates python, which creates all sorts of problems. Make sure to add python=3.6 to the list of packages passed to conda install and it should work ok!

Hi, my name is Ted. I tried running your code and encountered the following error. Would be grateful if any of you could help me figure it out. I got the error while running simtk.testInstallation.main().

Failed to import OpenMM packages; OpenMM will not work.
Make sure OpenMM is installed and the library path is set correctly.

Error message: cannot import name '_openmm' from 'simtk.openmm' (/usr/local/lib/python3.6/site-packages/simtk/openmm/init.py)
An exception has occurred, use %tb to see the full traceback.

SystemExit: 1

Hi @drcube98-mrss! Colab has changed a bit its internals but I didn't update this notebook. Take a look at my condacolab project for a new updated workflow. You can see an example here.