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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