Caculating electrrostatic potential over distance about pdb2pqr

[jbardhan]

Hi,

What do you mean by "of each component"?

From what I understand at the moment, it sounds like you're looking for the "write" command in the APBS input file, whose documentation is here: https://apbs.readthedocs.io/en/latest/using/input/old/elec/write.html?highlight=write

If you use the "write" command, in order to compute the average electrostatic potential at a particular distance from the GNP center, you'd need to do some post-processing.

If you can add some more details as to what components you are interested in calculating, we may be able to offer additional guidance.

Thanks very much,
Jay

[hanahg]

Hi again and thank you very much for the replay. The gild nano particles I prepared are composed of core Au atoms, AU atoms at the surface in which some of them are connected to a ligand by S atom. The ligand and the size of each GNP are different with different charges : positive, negative and without charge. They are neutralized by ions: CL and NA. The simulations are done in water environments. So, I should have some curves of electrostatic charge by distance from the center of GNP, including NP, WATER, IONS. And may be ST.... I should calculate the zeta potential as well; therefore, I would prefer to use your method if it is possible I appreciate your help. If you need more information or any file let me know. Sent from Outlook for Android<https://aka.ms/AAb9ysg>

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________________________________ From: Jaydeep Bardhan ***@***.***> Sent: Wednesday, November 29, 2023 5:57:34 PM To: Electrostatics/pdb2pqr ***@***.***> Cc: hanahg ***@***.***>; Author ***@***.***> Subject: Re: [Electrostatics/pdb2pqr] Caculating electrrostatic potential over distance (Issue #374) Hi, What do you mean by "of each component"? From what I understand at the moment, it sounds like you're looking for the "write" command in the APBS input file, whose documentation is here: https://apbs.readthedocs.io/en/latest/using/input/old/elec/write.html?highlight=write If you use the "write" command, in order to compute the average electrostatic potential at a particular distance from the GNP center, you'd need to do some post-processing. If you can add some more details as to what components you are interested in calculating, we may be able to offer additional guidance. Thanks very much, Jay — Reply to this email directly, view it on GitHub<#374 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AI5LF65NG2QV6PLIQNBKABTYG5SP5AVCNFSM6AAAAAA77PK256VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMZSGMZTIOJTHA>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[jbardhan]

Ah, I understand now I think, thank you.

Here's what I hear you saying:

1. You have created atomistic models of several gold nanoparticles, which are functionalized with different ligands.

2. The atomistic models assign various charges to the different atoms in each functionalized nanoparticle.

3. You desire to understand the electrostatic properties of these functionalized nanoparticles in an aqueous solution with some finite concentration of Na+ and Cl- ions.

4. The electrostatic properties of interest in any one system are (A) the average charge density as a function of radial distance from the center of the nanoparticle; and (B) the average electrostatic potential as a function of radial distance from the center of the nanoparticle. Ideally you would also like to calculate (C) the zeta potential of each nanoparticle, which is (in one particular terminology) the electrostatic potential at the "slipping plane."

If this is correct, I would suggest the following approach:

1. Use three separate APBS "write" commands. (A) "write charge" for the NP/ligand charge density; (B) "write ndens" or "write qdens" for the total charge density of mobile ions in solution; (C) "write pot" for the electric potential.

2. Post-process -- depending on your particular application you may want to add (A) and (B) for a "total" charge density. (I'd recommend checking such a result against "write edens" but that's only possible if you're using multigrid)

3. Post-process -- perform radial averaging (you may opt not to do this, and instead just look at, say, (X, 0, 0) but I recommend not doing that, due to grid sensitivities) on both the charge density/charge densities, and the electric potential.

4. Decide on what definition of slipping plane or zeta potential is appropriate for your application and research community, and calculate it from the radially averaged functions.

Does this address your questions?

Thanks very much,
Jay

[hanahg]

Hi,
Thank you for suggestions.
I am new to using APBS. I should read the guid carefully and try to do.
If I faced any problem, I will come back to you.

Thank you in advanced