From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Thu May 09 2013 - 01:09:27 CDT
> Hi users,
> I have divided RC into four non-overlapping windows each of width 3.5
> A spanning distance from 2.5 A to 16.5 A.
> Now, I have a question regarding convergence in each window. I can
> sense in some windows, convergence is faster and in some its very slow.
> Is it a good idea to extend the trajectories for windows where
> convergence is slow ??
It is not only a good idea, but it is desirable. Depending on the ruggedness
of your free-energy landscape, diffusion in certain regions will be
in others. Over stretches of your reaction pathway, the collective
you chose can be more or less coupled to other, slow degrees of freedom,
thus, requiring more or less sampling towards convergence.
> Can we join windows ran for different lengths to get PMF using
inputPrefix. Yes. For one-dimensional profiles, pasting gradients by hand
is also an option. If they are continuous across the reaction pathway,
already a good sign of a converged calculation.
-- _______________________________________________________________________ Chris Chipot, Ph.D. Theoretical and Computational Biophysics Group Beckman Institute University of Illinois at Urbana-Champaign 405 North Mathews Phone: (217) 244-5711 Urbana, Illinois 61801 Fax: (217) 244-6078 E-mail: chipot_at_ks.uiuc.edu Christophe.Chipot_at_edam.uhp-nancy.fr Web: http://www.ks.uiuc.edu/~chipot http://www.edam.uhp-nancy.fr The light shines in the darkness, and the darkness has not overcome it. John 1:5. _______________________________________________________________________
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