**From:** Brian Bennion (*brian_at_youkai.llnl.gov*)

**Date:** Wed May 05 2004 - 18:18:19 CDT

**Next message:**Armen Poghosyan: "FATAL ERROR: Patch needed for tuple is missing."**Previous message:**Brian Bennion: "Re: question on self-diffusion constant of TIP3P water"**Maybe in reply to:**Brian Bennion: "Re: question on self-diffusion constant of TIP3P water"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hello Hyon,

At 298K water molecules have a molecular volume of 30.02 A^3 based on a

denisty of 0.997 g/mL, which is the value in the CRC handbook.

So 1260*30.02 = 37825.2A^3 for real water.

Your box size is 37705.5A^3 so the density may be a little larger than

0.997 g/mL.

lets assume the real water volume for a moment...

1260 * 18.015amu = 22698.9* 1.6603 = 37686.98367 / 37825.2 = 0.99643 g/mL

^^^^^^

||||||

conversion to mass from amu

The answer is pretty close to experiment.

If we use your box volume the density will be:

37686.98367 / 37705.5 = 0.9995 g/mL

which is larger than before.

I have seen changes in density smaller than this affect water diffusion.

So you could test this by redimensioning your box to the lower value and

monitoring the diffusion....

Regards

Brian

On Wed, 5 May 2004, Hyonseok Hwang wrote:

*> Hi, Brian
*

*>
*

*> The size of the simulation box is 31.5A x 31.5A x 38.0A and there are
*

*> 1260 water molecules. As a result, I guess the density is 1.00 g/cm^3.
*

*> I will greatly appreciate it if you give me any comments.
*

*> Thank you very much for your reply.
*

*>
*

*> -Hyon
*

*>
*

*> Brian Bennion wrote:
*

*>
*

*> > Hi Hyon,
*

*> >
*

*> > How big was your box of water? The diffusion values are HIGHLY dependent
*

*> > on density. So I would like to ask how you determined the density?
*

*> > I am happy to see that your results are so reasonable, I too have only
*

*> > seen high values for TIP3P...
*

*> >
*

*> > Regards
*

*> > Brian
*

*> >
*

*> >
*

*> > On Wed, 5 May 2004, Hyonseok Hwang wrote:
*

*> >
*

*> >
*

*> >>Dear all,
*

*> >>
*

*> >>I carried out an MD simulation to obtain a self-diffusion constant of
*

*> >>water. I used TIP3P water model at 298K with NVT ensemble. The water
*

*> >>density is 1g/cm^3. I used the Einstein equation for diffusion constant
*

*> >>and the number I got was 2.7x10^-5 cm^2/s. I also found a similar number
*

*> >>in a paper. However, the number of the diffusion constant for TIP3P,
*

*> >>which most people refer to is ~ 5.0 x 10^-5 cm^2/s for TIP3P. I don't
*

*> >>understand why there are two values for TIP3P diffusion constant.
*

*> >>It would be great if I get some tips on that.
*

*> >>Thank you very much.
*

*> >>
*

*> >>Best,
*

*> >>
*

*> >>Hyon
*

*> >>
*

*> >>
*

*> >
*

*> >
*

*> > *****************************************************************
*

*> > **Brian Bennion, Ph.D. **
*

*> > **Computational and Systems Biology Division **
*

*> > **Biology and Biotechnology Research Program **
*

*> > **Lawrence Livermore National Laboratory **
*

*> > **P.O. Box 808, L-448 bennion1_at_llnl.gov **
*

*> > **7000 East Avenue phone: (925) 422-5722 **
*

*> > **Livermore, CA 94550 fax: (925) 424-6605 **
*

*> > *****************************************************************
*

*> >
*

*> >
*

*>
*

*> --
*

*> =======================================
*

*> Hyonseok Hwang
*

*> Postdoctoral Fellow
*

*> Department of Chemistry
*

*> Northwestern University
*

*> 2145 Sheridan Rd.
*

*> Evanston, IL 60208-3113 USA
*

*> ---------------------------------------
*

*> Tel:(847)467-4987(O)
*

*> Email:danggi_at_northwestern.edu
*

*> =======================================
*

*>
*

*>
*

*****************************************************************

**Brian Bennion, Ph.D. **

**Computational and Systems Biology Division **

**Biology and Biotechnology Research Program **

**Lawrence Livermore National Laboratory **

**P.O. Box 808, L-448 bennion1_at_llnl.gov **

**7000 East Avenue phone: (925) 422-5722 **

**Livermore, CA 94550 fax: (925) 424-6605 **

*****************************************************************

**Next message:**Armen Poghosyan: "FATAL ERROR: Patch needed for tuple is missing."**Previous message:**Brian Bennion: "Re: question on self-diffusion constant of TIP3P water"**Maybe in reply to:**Brian Bennion: "Re: question on self-diffusion constant of TIP3P water"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Wed Feb 29 2012 - 15:38:38 CST
*