On Wed, Sep 10, 2003, Ulf Johansson wrote:
>
>
> I've downloaded the parameter files and from them I first got the impression
> that the Amber Tip3p model is flexible (because K values are given for both
> the OW-HW bond and HW-OW-HW angle). Now, did I get you right in that this
> "flexibility" is then restrained by the Amber program, using a procedure
> called SHAKE, to render the Tip3p model inflexible (in the sense that the
> relative distances and angles between atoms never change), and that this
> also extends to the Tip4/5p models?
This is correct.
>
> Also do you know why this restraining is done. Doesn't it remove the
> internal vibration energy modes from the Tip3/4/5p water models?
The purpose of the restraints is indeed to remove the internal modes of
motion.
>
> I yet don't have access to the Amber source code. Do you know of some other
> place, article or so, where I can find the parameters for the "flexible"
> description of the Tip4/5p models?
As far as I know, tip4p and tip5p were developed as rigid models, and that is
the way they are treated in Amber. But there are plenty of review articles
out there on force fields for water, so you can check this yourself. There
are some flexible "extensions" of the tip3p model.
...regards...dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Wed Sep 10 2003 - 16:53:01 PDT
