Re: Ewald size-dependence correction in FEP simulation of an electric dipole

From: Victor Kwan (vkwan8_at_uwo.ca)
Date: Thu Sep 13 2018 - 10:57:31 CDT

Hi Ali,

If you mean the system-size dependency, here is an interesting paper

https://pubs.acs.org/doi/10.1021/acs.jpcb.7b09861

Victor

On 9/12/2018 8:34 PM, Ali Mehdizadeh Rahimi wrote:
> Dear All,
>
> The problem that I’m interested in is to charge two naked
> Lennard-Jones particles to opposite unit charges (create a dipole),
> starting from zero charge to the two atom’s final charge (-1 and +1).
> I want to calculate the charging free energies of the dipole as I
> change the distance between the two atoms (and ultimately obtain a
> landscape of energy as a function of the distance between the two
> atoms to assess the accuracy of a continuum theory that I’m working on).
>
> I went through the FEP tutorial for charging a spherical sodium ion.
>
> The change that I made to the setup.pgn was to add another sodium segment:
>
> segment SOD1 {
>
> residue 1 SOD
>
> }
>
> segment SOD2 {
>
> residue 2 SOD
>
> }
>
> and wrote the outputs to setup.pdb and setup.psf files.
>
> I modified the resulting psf file:
>
> …
>
> 4 !NTITLE
>
> REMARKS original generated structure x-plor psf file
>
> REMARKS topology ../common/top_all22_prot.inp
>
> REMARKS segment SOD1 { first NONE; last NONE; auto angles dihedrals }
>
> REMARKS segment SOD2 { first NONE; last NONE; auto angles dihedrals }
>
> 2 !NATOM
>
> 1 SOD1 1SODSODSOD-1.00000022.98980
>
> 2 SOD2 2SODSODSOD1.00000022.98980
>
> ….
>
> and the pdb file (e.g. for when the distance between the two
> oppositely charged atoms, d, is 6 A):
>
> REMARK original generated coordinate pdb file
>
> ATOM1SOD SOD1-3.0000.0000.000 -1.000.00SOD1 NA
>
> ATOM2SOD SOD23.0000.0000.000 -1.000.00SOD2 NA
>
> END
>
> and then solvated the dipole in a water box using solvate plugin of
> VMD and modified solvate.pdb:
>
> CRYST1**46.00046.00046.00090.0090.0090.00 P 11
>
> ATOM1SOD SOD S1-3.0000.0000.0001.001.00SOD1 NA
>
> ATOM2SOD SOD S23.0000.000 0.0001.001.00SOD2 NA
>
> ATOM3OH2 TIP3W5-19.332-9.918-4.0961.000.00WT1O
>
> ATOM4H1TIP3W5-19.776-9.549-4.8991.000.00WT1H
>
> ATOM5H2TIP3W5-19.908-9.621-3.3731.000.00WT1H
>
> ….
>
> ….
>
> and saved as solvate.fep.
>
> Finally equilibrated the system and ran forward and backward simulations.
>
> What would be the right expression to estimate the error due to the
> size-dependence of the energy to the system in my problem since the
> box is already charge-neutral?
>
> Thanks a lot for taking the time,
> Ali
>

what are you harping on about? Dipole and dipole moment are two separate
concept.

On 9/13/2018 12:16 AM, Nassar, Omneya wrote:
> Hello Ali,
>
> Thank you for your question. I would like to correct some misunderstandings you may have before addressing your problem at hand.
>
> 1. A dipole moment can only happen between two atoms covalently bonded and the difference between the partial charges of each atom is 0.5 or greater. Because sodium ions form ionic bonds instead of covalent bonds, their interactions are purely electrostatic and van der Waals interactions (nonbonded)
>

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