[gmx-users] Regarding viewing Trajectories

Mark Abraham mark.j.abraham at gmail.com
Wed Apr 5 08:37:39 CEST 2017


A peak in a distance distribution function by definition is contributed to
by lots of molecules around that distance from lots of different central
points. There's no single frame for each point.

If you look at a normal histogram, and see a peak, asking "which single
data point made this" is not meaningful, because multiple data points have
normally contributed.


On Wed, Apr 5, 2017 at 6:40 AM Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> Hello.,
> In RDF of amino acid with ammonia and water mixture, i have got a 1st peak,
> 2nd peak (solvation shell), and i need to view this in the vmd by making
> use of the trajectories (trr/xtc files), so while viewing the trajectories
> 1] how can i view that exact trajectory at which i have got the particular
> peak in RDF (since that would mean either H-bond formation/probability of
> tht molecule close to that)
> because viewing each frame to find it would take literally lot of time, ...
> Thank you.
> --
> With Best Regards,
> Ph.D Student
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