[gmx-users] Gmx hbond

Justin Lemkul jalemkul at vt.edu
Sun Apr 15 16:47:47 CEST 2018

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

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340 West Campus Dr.
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