From: LEWYN LI (ll2150_at_columbia.edu)
Date: Fri May 05 2006 - 12:35:09 CDT
Dear Binquan,
Since I know little about simulations of material, I found your
points quite interesting. Just a simple question: in simulations of
material, why does the speed of sound determine the time scale for the
signal? I would have guessed that the time scale depends on the physical
process you are interested in - the larger the process, the longer the
time scale. Could it be that the transfer of stress in material is
somehow related to the propagation of acoustic waves in the sample,
therefore the time scale of stress is determined by the speed of sound?
Anyway, my two cents about temperature and pressure control in
biomolecular simulations: in order to determine if your biomolecular
system is overdamped, you could try to estimate the frequency (or
relaxation time) of the motion that you are interested in. For example,
bond vibrations typically have a period of tens of femtoseconds, depending
on the nature of the bond. This would give you some idea about how much
damping you should use so that your system is not overdamped.
Also, you could just run a NVE simulation i.e. no temperature or
pressure control. Then you don't need to worry about overdamping at all.
LEWYN
On Fri, 5 May 2006, 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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