[gmx-users] Different results from identical tpr after MD
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Fri Apr 6 07:21:33 CEST 2012
Dear Acoot:
The idea of convergence is this: start a large number of simulations
from different conformations, analyze some quantity over time in each
simulation, and when the deviation of the average value of that
quantity from each separate simulation is less than the time-variance
within individual simulations, then you can imply that the simulations
have converged -- that is, the results of independent simulations
which started as different are now similar.
There is a huge body of work that uses a single simulations and
evaluates its so-called convergence using some assumptions and special
methods. That can also be very useful, but I find it informative to
think of "convergence" in its standard non-scientific dictionary
definition as the coming together of previously disparate things.
For simulations, my working definition is this: a set of simulations
has converged the value of some variable when the simulations were
initiated from sufficiently distinct conformational basins and then,
over time, the ensemble distribution of the time-averages of the
specified variable has a variance that is the same as the mean
time-averaged variation within independent simulations. The weak point
here is the part about "sufficiently distinct conformations", but I am
not sure that this can be stated less vaguely in the general case.
Chris.
-- original message --
Hi Justin,
Can you give me your definition of converged MD and unconverged MD?
Cheers,
Acoot
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