[gmx-users] interaction energy of bulk TIP3P

[sandeep somani]

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
discrepancy.

is there a way to get the full interaction energy with PME ?

thnx for the reply
-sandeep



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
> PME
> > for 400 ps and extracted the interaction energy of a randomly picked
> water
> > molecule with rest of the system.
> > Simulation was done at 298K and 1bar and usual procedure for generating
> a
> > 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
> in
> > the range of -81 +/- 1 kJ/mol i.e. ~11 kJ/mol less.
> >
> > any clues on origin of this discrepancy ?  relevant .top , .mdp files
> are
> > 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
> energy.
>
> Mark
>
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