Justin A. Lemkul wrote:
Rebeca García Fandiño wrote:
Thanks a lot for your answer.
My system have about 29000 atoms, and the simulation time was 1ns.
I have generated the error bars, and indeed you were right, they are
too big. The histograms looked good, so I thought they should be
well-converged...:S
What should I do, extending the simulation or generating more windows?
The simulations probably need to be longer. I've gotten good
convergence in much larger systems using far fewer windows but somewhat
longer simulations.
Another thing to consider (aside from my offhand guesses of simulation length)
is that if you're generating velocities at the beginning of each simulation in
each window in the absence of prior equilibration, you're not *really* getting 1
ns of viable data. Some should be discarded as equilibration, if you're not
doing that already. If you've done prior equilibration in each window, then
disregard this thought.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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