[gmx-users] interaction energy of bulk TIP3P
mark.abraham at anu.edu.au
Sun Nov 18 02:18:38 CET 2007
> Hi All
> I simulated a cubic box of 2180 TIP3P water molecules using gmx 3.3 and PME
> for 400 ps and extracted the interaction energy of a randomly picked
> molecule with rest of the system.
> Simulation was done at 298K and 1bar and usual procedure for generating
> water box and equilibration were used.
> Average interaction energy reported in the log file was
> Epot (kJ/mol) Coul-SR LJ-SR
> WAT-rest -8.13828e+01 1.21886e+01
> giving a total of -8.13828e+01 + 1.21886e+01 = -69.194 kJ/mol
> Comparing with published numbers using other MD programs this should be
> the range of -81 +/- 1 kJ/mol i.e. ~11 kJ/mol less.
> any clues on origin of this discrepancy ? relevant .top , .mdp files
The PME algorithm does an approximation to the full periodic Coulomb
summation, but does so with a calculation in direct space, as above, and
another in reciprocal space, where your energy groups are not meaningful.
So you're only getting the direct-space component of the interaction
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