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#compchem

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Piia Bartos

Reviewer #2 said my 80 ns simulations are too short.

I would also like longer simulations. However, I simulated the whole RNA Polymerase I complex with DNA with about 800k atoms. Which is far larger than usual systems in MD simulations. If I wanted microsecond scale simulations for this system, I would need months of calculation time. Furthermore, the simulations were not the main point of the story, they just supported the experiments...

#compchem#science#reviewer2
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Robert Pollice

#RobSelects preprint of the week #ChemRxiv: Modified independent gradient model approach for revealing non-covalent interactions based on promolecular densities. #compchem doi.org/10.26434/chemrxiv-2025

ChemRxivGraphically revealing weak interactions in dynamic environments using amIGM methodVisualization of weak interactions is now a very popular kind of analysis methods, which allows chemists to recognize existence, strength, and type of interactions in different regions of a chemical system easily and intuitively. Among these analysis methods, the independent gradient model (IGM) and its variant with better graphical effect, namely IGM based on Hirshfeld partition of molecular density (IGMH), are particularly useful. They can clearly reveal various interactions between specific fragments, and become widely popular in recent years. This chapter first briefly reviews the definition and characteristics of the two methods, and then introduces a new variant of IGM, called modified IGM (mIGM), which, like IGM, only requires atomic coordinate information to perform the analysis and thus the computational cost is fairly low, while its graphical quality in exhibiting weak interactions is almost as good as the markedly more expensive IGMH. This chapter then introduces the averaged mIGM (amIGM) method, which extends mIGM to visual analysis of the weak interactions involved in molecular dynamics trajectories. A series of examples fully demonstrate that amIGM can well display all kinds of weak interactions in dynamic environments, and its image quality and flexibility are all superior to the previously proposed averaged noncovalent interaction (aNCI) method with similar uses.
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