normal Martinize2 for Solvated System

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1 year 3 weeks ago - 1 year 3 weeks ago #9281 by mason
Martinize2 for Solvated System was created by mason
Hello,

My all-atom system is a protein solvated in TIP3P water, and I would like to use Martinize2 to CG the entire system. Is this currently possible? Or is there a different tool to solvate natively in Martini3?

I tried a few passes with Martinize2 before it occurred to me that the 4:1 W:HOH bead ratio might take a little more work than the relatively straightforward mapping of an amino acid.

Thanks in advance!

Mason

Edit:
I see the solvation method here, which I will try. My question remains though whether there is a way to Martinize existing solvent rather than de-solve and re-solve the Martinized system.
cgmartini.nl/images/stories/workshop2021..._3_protein_part1.pdf
Last edit: 1 year 3 weeks ago by mason. Reason: see edit note

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1 year 3 weeks ago #9282 by riccardo
Replied by riccardo on topic Martinize2 for Solvated System
Hi Mason,
Systems containing multi-molecule solvents like water are indeed usually de-solvated before Martinizing them and re-solvated at Martini resolution. As you noticed, grouping water molecules is not so straightforward, and the de-solve + re-solve works OK - so AFAIK everybody does the latter.

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1 year 1 week ago #9295 by mason
Replied by mason on topic Martinize2 for Solvated System
Thank you!

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