From: Binquan luan (bqluan_at_uiuc.edu)
Date: Fri May 05 2006 - 13:08:39 CDT
Yes, signals in materials or proteins propagate as acoustic waves. The
time scale is determined by length scale of process dividing sound
speed. So, larger process leads to a larger time scale normally.
Thanks for your suggestions. I guess that the time scale of bond
vibration gives a low bound of processes interested. There maybe long
wave modes associated with conformational changes in protein.
On Fri, 2006-05-05 at 13:35 -0400, LEWYN LI wrote:
> 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.
> 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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