From: Binquan luan (bqluan_at_uiuc.edu)
Date: Fri May 05 2006 - 10:39:27 CDT
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
>
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