Re: modelling an aqueous solution of protein+hydrogen peroxide

From: Lucas Neumann (
Date: Wed Jan 15 2020 - 18:27:29 CST

I don't think VMD plugin auto ionize is the best tool for this kinda of
problem. You probabily better off just using Packmol -- more suitable to
create system w/ solvente mixtures. Also, if your intented H2O2
concentration is low, you can always add them by hand.

Best regards

Em qua, 15 de jan de 2020 20:52, Artur Hermano <>

> Hello NAMD team,
> I am trying to model a protein in a water box with a fixed concentration
> of hydrogen peroxide.
> Is it possible to do so through the Autoionize wizard in VMD?
> Would somebody please give me any advice on how to set this up?
> Thank you so much!
> --
> Artur

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