Previous Thread
Next Thread
Print Thread
why TIP3P water model?
#6805 05/23/05 06:51 PM
Joined: Nov 2003
Posts: 54
firer Offline OP
Forum Member
OP Offline
Forum Member
Joined: Nov 2003
Posts: 54
Hi, I am just wondering that why CHARMM uses TIP3P model to represent water molecules. As compared with SPC/E model, the diffusion coefficient is too high 5.6x10-5 cm2/s as compared with bulk 2.3x10-5 cm2/s. The g(r) of Oxygen-oxygen is lack of the second peak.
So, anybody can tell me the reason what is advantage of TIP3P?

Re: why TIP3P water model?
firer #6806 05/23/05 07:41 PM
Joined: Sep 2003
Posts: 8,470
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,470
I've been told that with the 104 deg H-O-H angle TIP3P has slightly better structural and thermodynamic properties than SPC or SPC/E models (which have their own flaws). Another reason is that all of the CHARMM protein, nucleic acid, lipid, carbohydrate, etc., parameters have been developed wrt. to the TIP3P water model. The most promising (but costly) development is the TIP4Pew water model; diffusion is much improved, and the model is close enough to TIP3P that it should be a reasonable change for use with CHARMM macromolecule parameters.


Rick Venable
computational chemist

Re: why TIP3P water model?
rmv #6807 05/23/05 09:11 PM
Joined: Nov 2003
Posts: 54
firer Offline OP
Forum Member
OP Offline
Forum Member
Joined: Nov 2003
Posts: 54
no offense. Could you give me more detail of the comparsion of SPC/E and TIP3P? what kind of structure and thermodynamics properties of TIP3P are better than SPC/E model? or do you have any reference for recommend?
According to the Nilsson's paper [J. P. C. A 105, 9954, 2001], overall I feel that SPC/E is better than TIP3P.

Quote:

I've been told that with the 104 deg H-O-H angle TIP3P has slightly better structural and thermodynamic properties than SPC or SPC/E models (which have their own flaws). Another reason is that all of the CHARMM protein, nucleic acid, lipid, carbohydrate, etc., parameters have been developed wrt. to the TIP3P water model. The most promising (but costly) development is the TIP4Pew water model; diffusion is much improved, and the model is close enough to TIP3P that it should be a reasonable change for use with CHARMM macromolecule parameters.



Re: why TIP3P water model?
firer #6808 05/24/05 01:12 AM
Joined: Sep 2003
Posts: 8,470
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,470
Both Epot and P (Table 5) are better for TIP3P than for SPC/E, from Mark and Nilsson J Comput Chem 23: 12111219, 2002. CHARMM parameters have been designed for solvation with TIP3P; you can't just decide to use SPC/E without major testing and revision of all of the existing CHARMM parameters.


Rick Venable
computational chemist

Re: why TIP3P water model?
rmv #6809 05/24/05 04:00 AM
Joined: Nov 2003
Posts: 54
firer Offline OP
Forum Member
OP Offline
Forum Member
Joined: Nov 2003
Posts: 54
many thanks rmv for explaination.

Re: why TIP3P water model?
firer #6810 05/24/05 05:32 PM
Joined: Sep 2003
Posts: 8,470
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,470
I should add that we've been unhappy with the TIP3P self diffusion, which is even worse for Ewald methods; the viscosity is also off by a factor of 3 or more. We always have to independently estimate rotational diffusion of solutes when attempting to compute NMR T1's from solution simulations. We are investigating and are optimistic about the water model described in

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew
Hans W. Horn, William C. Swope, Jed W. Pitera, Jeffry D. Madura, Thomas J. Dick, Greg L. Hura, and Teresa Head-Gordon
J. Chem. Phys., 120:9665-9678 (2004)

As the name of the model implies, it's an adaption of Jorgensen's TIP4P model, revised for use with Ewald summation methods. The improved properties may be worth the extra computational cost of using a 4-site water model.


Rick Venable
computational chemist

Re: why TIP3P water model?
rmv #6811 03/03/08 06:37 PM
Joined: Oct 2004
Posts: 22
L
leo Offline
Forum Member
Offline
Forum Member
L
Joined: Oct 2004
Posts: 22
Hi, as the CHARMM force field is parameterized for TIP3P, will there be any side-effect if we use TIP4P-Ew instead of TIP3P?

Thanks!

Re: why TIP3P water model?
leo #6812 03/04/08 12:03 AM
Joined: Sep 2003
Posts: 8,470
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,470
I'd imagine that there could be consequences; I'm not aware of any detailed tests of the solvation properties of TIP3P vs. TIP4Pew, although I haven't been looking for any.


Moderated by  alex, lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.009s Queries: 30 (0.003s) Memory: 0.9516 MB (Peak: 1.0669 MB) Data Comp: Off Server Time: 2020-07-14 07:58:09 UTC
Valid HTML 5 and Valid CSS