Dear AmberUsers!
I want to calculate the potential Energy of a single Watermolecule by
hand. (Just to understand what Amber is doing.) I am using the
TIP3P-Model. According to the Literature by Jorgensen
<
https://doi.org/10.1063/1.445869>, which is cited by the Ambermanual,
the O-H-Bond and the H-O-H-angle are constant, but in the simulation
both are variable (for temperature above 0K), therfore Amber has to use
a non-rigid model, which extends the TIP3P-Model. But in the
AmberManaual I just found two pages about Solvent-force-field in "3.5.
Solvents", but I wasn't able to find neither any potentialfunktion nor
any useful reference.
I load source /leaprc.water.tip3p/ in LEaP, which loads /loadAmberParams
frcmod.tip3p/. This file has the TIP3P-Bond-parameters, but I cannot
find the equation (is it Lennhard Jones, is it a Morse-Potential, is it
a harmonic Potential,...). It tried Lennhard Jones and the harmonic
Potential, which are two-parameter-potentials, but I wasn't able to
calculate the same potential Boundenergy EPtot=BOND, which was proposed
by AMBER.
Here is the file with the bond-parameters
> This is the additional/replacement parameter set for SPC/E water
> MASS
> OW 16.0
> HW 1.008 0.000
>
> BOND
> OW-HW 553.0 0.9572 TIP3P water
> HW-HW 553.0 1.5136 TIP3P water
>
> ANGLE
>
> DIHE
>
> NONBON
> OW 1.7683 0.1520 TIP3P water model
> HW 0.0000 0.0000 TIP3P water model
>
Any help/comment would be highly appreciated.
Best Regards
Johannes Kalliauer
PhD-Student (civil engineering) at TU Wien
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Received on Wed Dec 27 2017 - 05:30:04 PST
