[gmx-users] What is the relationship between simulation time

David van der Spoel spoel at xray.bmc.uu.se
Thu Nov 22 08:52:20 CET 2007

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 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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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