How to calculate 1. Abraham LSER to estimate thermochemistry at 298 K and 2. Group additivity method for solute descriptor estimation

[tmcf22]

Topic

General area which your question is related to.

• [ ] Running an RMG job. Specifically, I am interested in solubility calculations. Their descriptions can be found in chapter 15 in the documentation.

Context

I cannot seem to run a solvation calculation using RMG. I am new to the program, so it is likely I am missing something quite simple. I ran a test calculation: examples/ch3no2 to see if the program was working, and it was.

Question

How do I run solvation calculations? I am interested in almost everything described in chapter 15 - Liquid Phase Systems. I noticed the two files estimate_solvation_thermo_and_search_available_solvents.ipynb and temperature_dependent_solvation_free_energy.ipynb in the ipython/ directory, are probably what I will need to edit to run my own calculations, but I cannot get them to successfully run.

Installation Information

I installed RMG using the Alternative Install: Binary Installation Using Anaconda. I am running Ubuntu 22.04 in a VM. I have plenty of cores and RAM. I will install RMG on my purely Linux Ubuntu 22.04 machine in case there are issues with using a VM, but I honestly do not know where to begin with solvation-thermo calculations. Thanks!

[JacksonBurns]

You might be able to get at least some of what you need via RMG-website, at this link: https://rmg.mit.edu/database/solvation/search/

Those two demonstration notebooks are Jupyter notebooks, which can be run using the jupyter package that is automatically installed with RMG. To do this, run jupyter notebook from the directory where you have RMG installed. I'm not sure exactly how this will work on a VM, but would be happy to help with any specific issues.

Please also take a look at the example input files in that chapter of the documentation, which should familiarize you with the mechanics of running RMG with solvated species.

[tmcf22]

Thank you very much! Yes, I need to get more familiar with all of the documentation in general. I am a little overwhelmed trying to learn Python and RDKit at the moment, but it will get better with time. Thanks again!

On Thu, Jun 13, 2024 at 3:12 PM Jackson Burns @.***> wrote:

You might be able to get at least some of what you need via RMG-website, at this link: https://rmg.mit.edu/database/solvation/search/

Those two demonstration notebooks are Jupyter notebooks, which can be run using the jupyter package that is automatically installed with RMG. To do this, run jupyter notebook from the directory where you have RMG installed. I'm not sure exactly how this will work on a VM, but would be happy to help with any specific issues.

Please also take a look at the example input files in that chapter of the documentation, which should familiarize you with the mechanics of running RMG with solvated species.

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[JacksonBurns]

Sure thing, good luck!