normal Dry Martini aggregation

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1 year 2 months ago #5877 by debaduttaprusty
debaduttaprusty created the topic: Dry Martini aggregation
Hi,
I am looking for PMFs for amino acid pairs (interaction matrix), which the Dry Martini paper claimed to be available upon request.Please let me know who I need to contact to obtain this data.

Also, do you have any suggestions regarding how one should go about modelling protein-polymer assembly using implicit solvent ? Since the well depths are higher in magnitude in Dry Martini than in wet Martini, this may lead to aggregation of molecules, a conclusion also drawn by the authors in the section "Limitations of the model". Is explicit solvent the only way to go? My system has around 1.2 million atoms out of which around 1.1 million are solvent atoms.

Thanks,
Debadutta

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1 year 2 months ago #5890 by peterkroon
peterkroon replied the topic: Dry Martini aggregation
Hi Debadutta,

For the future, you can contact a paper's corresponding author directly (in this case prof. Marrink). So please just send him an e-mail.

As to whether your system can be studied with dry martini, I'm not completely sure since proteins are too sticky. It depends a bit on your system and what you want to see/study.
You can try to make a small system with your protein and polymer which you study with both wet and dry Martini, so you can confirm you reproduce the relevant properties.

Good luck,
Peter

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