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

David van der Spoel spoel at xray.bmc.uu.se
Thu Nov 22 07:56:36 CET 2007

Mark Abraham wrote:
> Q733 wrote:
>> Dear gmx-users, I have a basic question to propose: What is the 
>> relationship between simulation time and the actual time a real process 
>> occurs? Are they the same? Or do they have certain correlation in 
>> certain situation?
> That depends how good a model of reality your simulation is. The only
> way to demonstrate that you have a model where simulation time might
> correspond to actual time is to find some suitable experimental data,
> and do a simulation that demonstrates such correspondence. Then you need
> to be able to justify extrapolating from that correspondence to
> correspondence for some system where you don't have experimental data.
> The practical problem here is that there are not all that many sources
> of accurate experimental data relating to time-scales of processes that
> are of phenomena exhibited by a "small enough" physical system to permit
> an accurate MD simulation to measure the same quantity for a reasonable
> expenditure of computer time. I can't think of any off-hand, but maybe
> others can.
Yes, there are plenty, for instance diffusion, and rotational 
correlation times. Both can be related to e.g. NMR experiments. In 
modern force fields the correspondence is quite good, within a factor of 
two for water, arguably one of the most difficult substances to model 
(been there, done that).

Of course it depends on what kind of process you're interested in, but 
even rates for protein folding are within this factor or two or so, 
although there are not that many simulations out there that tried to 
measure it (look for work by the Pande group for some examples).

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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