# Re: sound velocity of water

From: Binquan luan (bqluan_at_uiuc.edu)
Date: Fri May 05 2006 - 14:41:08 CDT

Hi Marc,
The idea is to measure the volume vs. pressure curve for a box of TIP3
water at constant temperature. It will give me the bulk modulus K of the
water. Then I can use formula Sqrt[K/density] to estimate the sound
velocity.

But the big pressure fluctuations may or may not cause trouble. I asked
a question on pressure fluctuations before and I found that pressure is
very constant without electrostatic interactions. I guess that I will
get quite constant volume and pressure after a long time average.

Please let me know if you or anyone else has a better idea.
Thanks,
Binquan
On Fri, 2006-05-05 at 13:56 -0400, Marc Q. Ma wrote:
> Can you describe your idea of measuring sound speed using MD
> simulations?
>
> I would guess sound speed in protein solutions is about same as in
> water or soft body tissue as body contains large percentage of water,
> 1500-1600 meters/second (in water it is 1540 m/s).
>
> If you indeed can measure sound speed through MD simulations, for a
> solvated protein system, the properly damped system should allow
> sound to travel at the same speed as in pure TIP3P water.
>
> cannot believe i am trying to answer a question that is the weirdest!
>
> marc
>
> On May 5, 2006, at 11:39 AM, Binquan luan wrote:
>
> > Glad to win a prize.:) Thanks. Let's discuss it further.
> >
> > I am new to simulations of biology system. From my previous experience
> > in simulations of material, it is important for one to know the
> > speed of
> > sound in your system. It set the time scale for signal (like
> > stress) to
> > propagate through the simulation system. Thermostat or press
> > control are
> > usually used in the simulations. The damping time scale in
> > thermostat or
> > press control should be larger than the time scale for signal to
> > propagate through the system. Otherwise, the system is overdamped. For
> > example, a protein could move in certain time scale if not overdamped.
> > Please correct me if I am wrong.
> >
> > In short, knowing the speed of the sound in your simulation system
> > give
> > you some ideas on whether the system is in the overdamped region or
> > not.
> >
> > I could set up a simulation to measure the speed of sound in a box of
> > Tip3 water molecules. But I appreciate if anyone who already knows it
> > could tell me.
> >
> > Binquan
> >
> > On Thu, 2006-05-04 at 17:25 -0700, Richard Law wrote:
> >> And the prize for the weirdest question to make the NAMD list goes
> >> to . .
> >> .
> >>
> >>
> >> On Thu, 4 May 2006, Binquan luan wrote:
> >>
> >>> Dear all,
> >>> Does anyone know the sound velocity in the water using Tip3
> >>> model? What
> >>> would be the sound velocity in protein normally? An approximate
> >>> number
> >>> is enough.
> >>> Thank you very much,
> >>> Binquan
> >>
> >>
> >> But you could read these:
> >>
> >> www.cs.purdue.edu/homes/voichi/JMBhydcomp.pdf
> >> http://en.wikipedia.org/wiki/Speed_of_sound
> >> http://scitation.aip.org/getabs/servlet/GetabsServlet?
> >> prog=normal&id=JCPSA6000123000010104503000001&idtype=cvips&gifs=yes
> >> http://scitation.aip.org/getabs/servlet/GetabsServlet?
> >> prog=normal&id=JCPSA6000122000005054902000001&idtype=cvips&gifs=yes
> >>
> >
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:01 CST