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normal How to use Martini3 to simulate a protein in ammonium chloride solution

  • Kalindu
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10 months 2 weeks ago #9652 by Kalindu
How to use Martini3 to simulate a protein in ammonium chloride solution was created by Kalindu
I am doing MD simulations of protein solutions under the presence of different salt. May I know, is any way to simulate a protein solution with ammonium chloride solution using the Martini3 force field?

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10 months 3 days ago #9658 by riccardo
Replied by riccardo on topic How to use Martini3 to simulate a protein in ammonium chloride solution
According to Supp. Table 25 of the Martini 3 Supp info ( static-content.springer.com/esm/art%3A10..._1098_MOESM1_ESM.pdf ), ammonium can be described by a TQ5p (+1) bead, while chloride by TQ5 (-1). Hence, that salt is covered.

Then you just need to be able to setup a protein simulation in Martini: see here for the most recent tutorials, a few of which involve setting up protein simulations: cgmartini.nl/index.php/2021-martini-online-workshop/tutorials

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  1. Force Fields
  3. Other Molecules
  5. How to use Martini3 to simulate a protein in ammonium chloride solution
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