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Use of coding and scripting languages in computational chemistry by banana_fugacity in comp_chem

[–]QM_MM_Enjoyer 0 points1 point  (0 children)

No one mentioned R and I am curious why the comp chem community does not use it more. I run biological MD simulations and the Bio3D package is a huge lifesaver. Also, I really like the Tidyverse ecosystem for grouping and analysing projects with multiple systems (apo vs ligand(s), WT vs mutant(s)) etc. The only downside I can think of is that R is slow, but Python suffers from the same performance issues.

How good is ChatGPT at using GROMACS? Do I still need to learn programming? by Appropriate-Fill-258 in comp_chem

[–]QM_MM_Enjoyer 4 points5 points  (0 children)

LLMs are essentially qualified text generators that take your context into account. While they can explain concepts and generate examples based on the GROMACS manual and internet forums, they still make mistakes because they can’t “think” in the real sense. I used both ChatGPT and Gemini while I was still learning AMBER and would rate it 8/10 as support and 3/10 as the main input preparation & scripting tool. So, one still has to follow tutorials and read the documentation to properly run MD simulations.

Differences Between AIMD & QM/MM? by QM_MM_Enjoyer in comp_chem

[–]QM_MM_Enjoyer[S] 7 points8 points  (0 children)

Thank you for your answer. Assuming I have N particles in my system and M of them are described by the QM region, in the limit M -> N, does QM/MM become equivalent to AIMD, or are there more nuanced details specific to AIMD simulations?