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Welcome to the pytraj wiki!

What's new in pytraj 1.0.0 (AMBER16)

• Support multiple parallelization schemes (multiprocessing, MPI)
• Integrate with biomolecular viewer in Jupyter notebook

Install

Using conda

• conda install -c pytraj pytraj-dev

github version

• if using the most updated pytraj version (recommended)
  • git clone https://github.com/pytraj/pytraj
  • cd pytraj
  • python ./setup.py install
• if using specific verion (go to releases to check the most updated and stable version)
  • wget https://github.com/pytraj/pytraj/archive/v0.1.2.dev4.tar.gz
  • (unzip and cd to pytraj)
  • python setup.py install
• Done
• Simple test: python -c 'import pytraj as pt; pt.run_tests()'

Note: Possible failure: can not find netcdf.h file. Make sure to install netcdeflib or specify its include path

Using pip

• not yet supported. Use "git" or "conda"

run small test after installing

python -c 'import pytraj as pt; pt.run_tests()'

if you install via github, you will get full test runs

• cd tests
• python ./python ./run_all_and_find_fails.py

Possible errors:

1. "ImportError: libcpptraj.so: cannot open shared object file: No such file or directory"

you need to add libcpptraj.so to LD_LIBRARY_PATH