AMBER Archive (2008)

Subject: RE: AMBER: Questions on TIP4P model?

From: Chin, Keith B (keith.b.chin_at_jpl.nasa.gov)
Date: Sat Nov 29 2008 - 17:43:21 CST

David:

Thank you. This really resolves a lot of our "head-scratching" on TIP4P model effort.

-keith

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of David A. Case
Sent: Saturday, November 29, 2008 11:21 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: Questions on TIP4P model?

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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