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.
________________________________________________________________________
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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