On 4/13/18 2:22 AM, rose rahmani wrote:

I have 2 questions, but please consider them 2 distinct questions and are
not related.
I did umbrella sapmling and calculate the PMF.
Now i I want to calculate number of hydrogen bonds for amino acid in its
initial distance(far from surface) and binding distance ( which is close to
surface and PMF is minimum there).
1- Is it rational to use pulling data(traj.xtc, .tpr,...) to calculate this
analysis, as it is nonequilibrium condition?

Sure. In each umbrella sampling window, you're restricting motion along a reaction coordinate, which allows you exactly compute distance-dependent properties.

2- Is it better to choose initial frame and binding frame, do umbrella
sampling step (, nvt) and calculate number of hbons separately and compare
the result? Is it true to compare them in this condition?

Using only the starting frame makes no sense. There's no reason to think that any single frame from any simulation is representative of the actual ensemble.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129


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