[Chimera-users] Solvate models

[Elaine Meng]

Hi Nikolay,
These are various representations of water molecules used in simulations -- they differ in geometry, partial charges, number of points and other technical aspects.  Chimera's Solvate tool is an interface to the solvate options in the AmberTools package, and although the AmberTools reference manual doesn't say much about these different models, it does give literature references for full details.The AmberTools12 reference manual (PDF) can be downloaded from
<http://ambermd.org/doc12/>
... see pp. 49-50, solvent models

According to that, the TIP3P model of water is the Ambertools default.

For a combined explanation of some of the water models, see wikipedia:
<http://en.wikipedia.org/wiki/Water_model>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco



On Apr 4, 2012, at 7:05 PM, Nikolay Igorovich Rodionov wrote:

> Hi all,
> I was wondering if some could explain to me the differences between the water models available under the solvate option.
>  
> 	• POL3BOX - POL3 water model
> 	• SPCBOX - SPC/E water model
> 	• SPCFWBOX - SPC/Fw water model
> 	• QSPCFWBOX - qSPC/Fw water model
> 	• TIP3PBOX - TIP3P water model
> 	• TIP3PFBOX - TIP3P/F water model
> 	• TIP4PBOX - TIP4P water model
> 	• TIP4PEWBOX - TIP4P/Ew water model
> Thank you all in advance,
> Nikolay Rodionov