Q733 wrote:
Thanks very much, what you have mentioned are situations which are
temperature fixed. How about the molecular rearrangement when
temperature is changed , for example, a lipidbilayer equilibrated at a
temperature and then put it at another temperature? I know when I do
this kind of simulations , it equilibrates after about 12 ns (the total
eneragy become unchanged). Is the real process of the same time scale?
Any suggestion will be appreciated, thanks in advance.
Think about it: in the simulation you can change the temperature
instantly, in reality this is difficult, unless you use a laser or
something like that. In addition you simulation system is very small
compared to what you could do experimentally. Larger things take more
time to equilibrate. If you make your simulation box 4 times as large
equilibration will probably take twice as long. After that however the
fluctuations will be half as large as your original box.
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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