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Create custom solvent
- zhenzey
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1 year 2 months 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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- riccardo
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1 year 2 months 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.
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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- zhenzey
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1 year 2 months 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!!
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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- riccardo
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1 year 2 days 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.
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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- JessieJim1
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11 months 3 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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