normal Create custom solvent

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1 year 1 month ago #9591 by zhenzey
Create custom solvent was created by zhenzey
Hi, I was wondering whether there is any way of creating custom solvents based on the SMILES of the chemical. Is "auto_martini"( github.com/tbereau/auto_martini ) a reliable way of doing it? Or we still need to follow the tutorial of parameterize a small molecule

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1 year 1 month ago #9592 by riccardo
Replied by riccardo on topic Create custom solvent
For Martini 2, there's also doi.org/10.1021/acs.jctc.1c00322 , that is more recent.

For Martini 3, no complete tools yet that I know of. So cgmartini.nl/index.php/2021-martini-onli...a-new-small-molecule would be the way to go.

Remember to validate the model with logP or other free energy of transfer data, and mass density.

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1 year 1 month ago #9593 by zhenzey
Replied by zhenzey on topic Create custom solvent
Thanks a lot for answering and sharing the paper. I am trying to generate my own solvents with these methods for peptide assembly in a high-throughput way.

I have compared the parameterization results of auto-martini with the existing solvents (e.g. ethanol, acetic acid). They give me different results and the assembled phases are different with these CG models. Therefore, I was wondering which methods are more accurate (existing solvents in Gromacs, auto-martini or the more recent one).

Also, I did not find any open-source code for the recent paper via a quick search. Do you know any of them? Thanks a lot again for your help!!

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11 months 3 weeks ago #9616 by riccardo
Replied by riccardo on topic Create custom solvent
Sorry, I missed the reply and found it while decluttering my email box.

1. Trust the validated solvent, if they exist. If they don't exist, validate the solvent model generated by auto_martini (compute at least the density; much better if you have any free energy of transfer data involving that solvent; also, make sure that the mapping that auto_Martini suggests makes sense in terms of the Martini mapping guidelines).

2. If I remember correctly they have the code in the SI of the paper.

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11 months 2 weeks ago #9621 by JessieJim1
Replied by JessieJim1 on topic Create custom solvent
auto_martini is a well-established tool in the field of molecular dynamics simulations, and it has been used in various studies to parameterize different types of molecules. So, it can certainly be a good starting point for your research.

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