[gmx-users] Coulomb Long range using PME

[benrezkallah djamila]

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