The potential is a Lennard-Jones potential, but as you observe there is no
interaction between the neighboring O and H atoms of one water molecule.
These are excluded interactions. The bonded potential is going to be very
slight if it even registers, because the SETTLE algorithm used with TIP3P
analytically resets the geometry of the water to equilibrium each time it
is moved. If you are doing this in a periodic setting, you will encounter
the long-ranged electrostatics, which for a single water molecule in a
medium sized box are still not zero.
On Wed, Dec 27, 2017 at 8:00 AM, Johannes Kalliauer <
johannes.kalliauer.tuwien.ac.at> wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 27 2017 - 06:00:04 PST
