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.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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