init.sh is not working

[reyhan akkaya]

Dear Westpa community,

I am new user of westpa. I am trying the NaCl-Namd tutorials on Linux cluster with anaconda. I installed the latest version of Westpa and Python3.10.  But ı am not able to run any westpa simulation. When ı run the init.sh, ı am getting this error and the west.h5 file is not created. 

echo $WEST_PYTHON 

/home/akkaya/anaconda3/envs/westpa2/bin/python3.10

-----------------------------------------

/home/akkaya/anaconda3/pkgs/westpa-2022.02-py310h5764c6d_0/bin/w_init: line 2: /home/conda/feedstock_root/build_artifacts/westpa_1657918010841/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python: No such file or directory
bash: --bstate-file: command not found...

-------------------------------------------

Thank you for your any help.

Best Wishes,

[Anthony Bogetti]

Hello,

Thanks for the question!  We are happy to help you get your WESTPA simulation up and running on your cluster.

Currently, the nacl_namd tutorial has not been updated to WESTPA 2.0 (the latest version of WESTPA), and only the OpenMM and Amber versions (basic_nacl and basic_nacl_amber) have been updated to be compatible with WESTPA 2.0.  We are currently working on updating the NAMD tutorial to be compatible with WESTPA 2.0 and will let you know once that is complete.

In the meantime, you could try to run the OpenMM version (basic_nacl) just to get familiar with WESTPA 2.0 and then switching to NAMD later will be fairly straightforward.

Please see here for the WESTPA 2.0 (and OpenMM) install instructions.  And please see here for the WESTPA 2.0-supported OpenMM tutorial.

Let us know if you have any additional questions.

Best,

Anthony

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[Jeremy Leung]

Hi Akkaya,

We have updated the NAMD tutorial to work with WESTPA 2.0 (v2022.XX).

Do note that this requires you to download the CHARMM36 force field files here into common_files/toppar and install mdanalysis into the same conda environment as westpa.  Like other tutorials, you will have to specify which environment to activate and provide the path to namd2 executable in `env.sh`.

Do let us know if you encounter any problems. We are happy to help.

Regards,

Jeremy L.