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On 15/02/2012 2:46 AM, Qiao Baofu wrote:
<blockquote
cite="mid:CAJPWMBefAG86vXojUDOeLFb-9ssqbhvqccx=g6TvbJA7aRZtig@mail.gmail.com"
type="cite">Hi all,<br>
<br>
Anybody can help me out! Thanks in advance?<br>
<br>
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".<br>
1. "coulombtype=PME"<br>
Coul. recip. -139.191 -- 0
0 (kJ/mol)<br>
Coul-SR:NA-CL <b>-0.0322805</b> --
0 0 (kJ/mol)<br>
LJ-SR:NA-CL -0.00100285 --
0 0 (kJ/mol)<br>
2. "coulombtype=cut-off"<br>
Coul-SR:NA-CL <b> -138.935</b> --
0 0 (kJ/mol)<br>
LJ-SR:NA-CL -0.00100285 --
0 0 (kJ/mol)<br>
<br>
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. <br>
However under "coulombtype=PME", how does Gromacs get the value of
-0.0322805kJ/mol for "<b>SR</b>" 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.<br>
</blockquote>
<br>
Your two atoms are within the cut-off distance, so their interaction
contributes to Coul-SR:NA-CL. The total energy for that interaction
is distributed over the Coul-SR and Coul. recip terms (which is how
PME works...), which you will note is approximately equal to Coul-SR
for coulombtype cut-off.<br>
<br>
By construction, your periodic images are too far away to contribute
to this term in either case (and you'd have been prevented by grompp
from getting this far, if that were not true).<br>
<br>
<blockquote
cite="mid:CAJPWMBefAG86vXojUDOeLFb-9ssqbhvqccx=g6TvbJA7aRZtig@mail.gmail.com"
type="cite">
<br>
Some details:<br>
Gromacs 4.5.5<br>
PBC is used.<br>
distance of Na^+ and Cl^-: 1nm<br>
Na^+ and Cl^- are frozen in XYZ dimensions.<br>
Only 1 step is run.<br>
</blockquote>
<br>
Using mdrun -rerun is often the best way to calculate single-point
energies/forces.<br>
<br>
Mark<br>
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