From: Marc Q. Ma (qma_at_oak.njit.edu)
Date: Fri May 05 2006 - 12:56:09 CDT
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
>>
>
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