[gmx-users] what does the "Coulomb (SR) mean under PME?

[Qiao Baofu]

Hi all,

Anybody can help me out! Thanks in advance?

In my test simulation, there are one Na^+ and one Cl^- (the distance of
1nm) in vacuum in a very big simulation box (10*10*10 nm^3). I calculated
the energies under two different conditions, "coulombtype=PME" vs
"coulombtype=cut-off".
1. "coulombtype=PME"
Coul. recip.               -139.191         --          0          0
(kJ/mol)
Coul-SR:NA-CL            *-0.0322805*         --          0          0
(kJ/mol)
LJ-SR:NA-CL              -0.00100285         --          0          0
(kJ/mol)
2. "coulombtype=cut-off"
Coul-SR:NA-CL             * -138.935*         --          0          0
(kJ/mol)
LJ-SR:NA-CL              -0.00100285         --          0          0
(kJ/mol)

I did some calculations. Under "coulombtype=cut-off", E(Coul-SR) =
f*e_i*e_j/r with f=138.935, which is what I expect.
However under "coulombtype=PME", how does Gromacs get the value of
-0.0322805kJ/mol for "*SR*" term? If I understand it correctly, "SR" means
"short-range", which is within the cut-off distance. Since the cut-off
distance (1.2nm here) is much smaller than the simulation box length
(10nm), there is not short-range interaction with the image box.

Some details:
Gromacs 4.5.5
PBC is used.
distance of Na^+ and Cl^-: 1nm
Na^+ and Cl^- are frozen in XYZ dimensions.
Only 1 step is run.

best regards,
Baofu
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