[gmx-users] interaction energy of bulk TIP3P
ssomani at gmail.com
Tue Nov 20 04:26:32 CET 2007
i see. i reran the trajectory with reaction field electrostatics and that
gave a more negative energy value which was closer to what i was expecting.
i guess the missing reciprocal space contributions explains this
is there a way to get the full interaction energy with PME ?
thnx for the reply
On Nov 17, 2007 8:18 PM, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> > Hi All
> > I simulated a cubic box of 2180 TIP3P water molecules using gmx 3.3 and
> > 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
> > below.
> 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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