On Wed, Dec 27, 2017, Johannes Kalliauer wrote:
>
> 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.
A single water molecule has zero potential energy in the TIP3P model: remember
that TIP3P is a rigid model, so you need to use SHAKE/SETTLE with it.
> therfore Amber has to use a non-rigid model, which extends the
> TIP3P-Model.
This is not correct. I think the only non-rigid water models that Amber
supplies parameters for are spcfw and qspcfw (where the "f" means flexible.)
This is described in Section 3.5 of the Amber 2017 Reference Manual.
As Dave Cerutti pointed out, if you have a perioidic system (i.e. more than
one water molecule), then the potential energy will not longer be zero. But
I'm guessing this doesn't apply to you.)
....dac
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Received on Wed Dec 27 2017 - 06:30:04 PST
