Installation Instructions

Installation Instructions

These are notes on how to install software, primarily for computational chemistry.


Just use conda, it will save you enormous amounts of time:

conda install -c rdkit rdkit

COSMO-RS on Linux

COSMO-RS is a fluid phase thermodynamics program. Usually, you use it from the GUI, COSMOthermX, but sometimes you need to run large numbers of calculations from on a server.

It's not immediately obvious how to install COSMOtherm (i.e., without the GUI) from the command line, so here's a step-by-step guide.

  1. Download COSMOtherm and, optionally, COSMObase (an add-on database with 12k+ extra molecules) from Biovia 3Dpassport download page. You should have a login from when you bought your license. I just installed the highest fidelity COSMObase files (TZVPD-FINE).
  2. image
  3. Copy the zip files for COSMOtherm and COSMObase onto your linux server. For example, replace USER@HOST with the username and address of your server and run the following command (removing the COSMObase file if you don't have it):
  4. scp USER@HOST:/home
  5. Unzip the files on the server and copy the COSMObase files to the correct location if you have them. Replace 2020 with whatever version you have.
  6. unzip
    # If you have COSMObase:
  7. Upload your license file to the server and copy it to the proper location:
  8. mkdir -p BIOVIA/COSMOtherm2020/licensefiles/
    cp license.txt BIOVIA/COSMOtherm2020/licensefiles/
  9. If you have any COSMObase files, you need to manually add them to the COSMOtherm XML configuration file:
  10. # Open the configuration file (can do this alternatively with vi, nano, etc.)
    vim BIOVIA/COSMOtherm2020/config/settingsLinux.xml

    Scroll down to the <AllDatabases> tag, and add your database. For TZVPD-FINE, you need the following:

         <DatabaseName selected="1">TZVPD-FINE-LARGE</DatabaseName>

    Then, under the SQLiteSettings tag, add the database to the correct level, so COSMOtherm knows to look for it:

    <DatabaseList parametrisation="TZVPD-FINE">
  11. To use cosmotherm from the command line, make sure to add it to your path. You can modify ~/.bash_profile or ~/.bashrc as follows:
  12. export PATH="~/BIOVIA/COSMOtherm2020/COSMOtherm/BIN-LINUX:$PATH"

    This assumes the BIOVIA directory is in your home directory. Put the reference anywhere you need it.

    As an alternative to using the command line, you can request a copy of BIOVIA's COSMOpy library, which allows you to call COSMOtherm from python.