[gmx-users] Coulomb Long range using PME

[Mark Abraham]

The long-ranged component of PME is fundamentally unsuited to
decomposition. Do something else.

Mark
On Nov 23, 2013 3:38 PM, "benrezkallah djamila" <benrezkallah at gmail.com>
wrote:

> Dear gmx-users,
> I have a problem with the calculation of the interaction energy using PME
> method.
> I know that this subject has been posted many times, but I'm still confused
> with some points.
> My system is consisting of a protein in solvent and counter ions : Na+ and
> Cl- .I try to calculate the coulomb (LR) between one residue of the protein
> ; (ASN) and The ions Cl- and Na+ respectively.
> So I have made groups in the .mdp file : ASN Protein(rest) Sol Na Cl
> I want to calculate the Coulomb (LR) between : ASN_Cl , ASN_Na and
> ASN_protein(rest).
> I have read some answers in the mailing list treating this subject; but I'm
> still confused with some questions
> 1) I know that the coulomb-recip value in the .edr file is the some of all
> the interaction energies between two groups specified in the .mdp file. and
> I must rerun my job setting the charge of some groups to zero to calculate
> the desired values, but since I use PME I have to ensure the charge
> neutrality of the system, and to calculate fo exemple E(lr)(Na_Na), I must
> put the charge of each the following groups: ASN, Protein(rest), Cl and Sol
> equals to zero. so I get
> for this job a total charge of the system equals to +43 (since I have 43
> Na+ ions in my system). How can I treat this?
> 2) My second question is since the .edr file gives the coulomb (recip.)
> term, how to calculate the coulomb (LR) from it?
>
> Thank you,
> Djamila Benrezkallah
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