From: Chris Chipot (
Date: Thu May 09 2013 - 01:09:27 CDT

Hi User,
> 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
faster than
in others. Over stretches of your reaction pathway, the collective
variable that
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
> inpuprefix??
inputPrefix. Yes. For one-dimensional profiles, pasting gradients by hand
is also an option. If they are continuous across the reaction pathway,
that is
already a good sign of a converged calculation.

Chris Chipot

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
The light shines in the darkness, and the darkness has not overcome it.
                                                               John 1:5.

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