AMBER Archive (2008)

Subject: Re: AMBER: Questions on TIP4P model?

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sat Nov 29 2008 - 13:21:01 CST

On Fri, Nov 28, 2008, Chin, Keith B wrote:
>
> 1. In amber amber9/dat/solvents/tip4p dir, there is a parm.top file of
> tip4p water. The atomic mass of the extra point, EPW, is 3.0 instead of
> 0.0. For what purpose was the EPW point assigned a value of 3.0?

As the 00_README files indicate, these are pretty old files. The mass of
extra points is ignored; I suspect the 3.0 value comes from some earlier times
(these files were made by Jim Caldwell in 2002) when extra points were handled
in a different fashion.

> 3. Most importantly. In xleap, I created sand parmtop and parmcrd file
> using frcmod.tip4pew and frcmod.tip model files.
> For tip4pew model the partial charges in the parmtop file are:
> O H1 H2 EPW
> 0.00000000E+00 9.55249411E+00 9.55249411E+00 -1.91049882E+01
>
> For tip4p model the partial charges in the parmtop file are:
> O H1 H2 EPW
> 0.00000000E+00 9.47559600E+00 9.47559600E+00 -1.89511920E+01
>

As Carlos explained, charges in a prmtop file are in internal units. If you
divide the EPW charge value of 18.951192 by 18.2223, you get -1.04, in units
of the electron charge.

TIP4P/EW is recommended over TIP4P itself for most Amber simulations. Be sure
you really want TIP4P itself if you do simulations with it.

....dac

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