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I'm now currently simulating the system in which charged peptide (ARG, LYS, ASP, GLU) is solvated in electrolyte solution. MD simulation was performed based on the AMBER14ffSB force field, but in here I'm not much sure whether this force field accurately models the peptide-ion interaction or not. For instance, trajectory shows a very strong binding between carboxylate ion (C-termini or ASP, GLU side-chain) and sodium ion. I once heard that there are some issues regarding such circumstances, as such some electrostatic interactions are too much overestimated compared to the experimental results. Below is the observed snapshot where blue particles are the sodium ion, coordinated with several carboxylate ions.

enter image description here

Is there any preferred force field in bio-MD community that is known to be superior to other one for capturing such electrostatic interaction? Any recommendation is highly welcomed!

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  • $\begingroup$ +1 and welcome to our new community! Thank you for contributing your question here and we hope to see much more of you in the future!!! $\endgroup$ Jan 30, 2023 at 17:45

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If you are looking at the interactions between a charged peptide and ions, I would recommend that you look into polarizable FFs that are available in literature. I know that OPLS and CHARMM have polarizable FFs available. They would generally give you better results because the charges are able to respond to the local environment.

Longer Answer:

  1. why additive FF is generally not suitable for investigating interactions between charged molecules and ions?

    additive FFs are generally based on fixed-point charges, which mean that they are unable to account for charge transfer, ion-dipole, ion-induced dipole or any of such interactions. It might happen that few interactions are over-represented or under-represented while using such FFs. CHARMM has a mechanism called NBFIX, where you override the original value in the parameter file with an updated value, that is more appropriate for some systems.

    Please note that the parameters are built to be transferable across multiple molecules, and it is impractical to build specific parameters for every system that we encounter.

  2. What improvement does use of Polarizable FF bring?

    Fair Note: I only have experience with Classical Drude polarizable FF in CHARMM, so I can comment only on that.

    In comparison to additive FF, Classical Drude polarizable FF has an extra particle (Drude particle) that helps in the capture of such interactions. Accurate capture of such interactions are important if you are looking at interactions between a charged molecule and an ion. You can refer to this paper to get a better understanding of why Drude is better than additive FFs.

    However, please note that employing Drude polarizable FF for your calculations would also mean that you would need to spend more computational resources at studying the same system, in comparison to additive FF simulations.

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    $\begingroup$ Thanks for your answer! I think I can follow your suggestions via OpenMM simulation package. $\endgroup$
    – Arete
    Feb 1, 2023 at 17:05
  • $\begingroup$ Great! OpenMM would be a wonderful choice $\endgroup$ Feb 1, 2023 at 17:09

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