On Fri, 2014-11-07 at 15:57 +0530, Mary Varughese wrote:
> sir,
>
> As per this link
> http://archive.ambermd.org/201007/0681.html
>
> ""atom# :res.atom atom# :res.atom atom# :res.atom %occupied
> > distance angle lifetime maxocc
> > | 115 :1.O10 | 104 :1.H20 92 :1.O8 | 96.06 2.818 ( 0.21)
> > 34.14 (28.58) 45.5 ( 72.3) 390 |....x.
> > .*..*...........*.x*...**.**.........*.....|
>
> The h-bond is formed for 96% of the simulation; average distance of 2.818
> A with a 0.21 stddev. The lifetime is 45.5 frames (i.e. if you assume 1
> ps between frames, the average lifetime of the h-bond is 45.5 ps; note
> that this value will depend on the distance cutofff). Finally the maxocc
> represents the longest time an h-bond was formed was 390 frames. You can
> likely see this as fluctuations in the distance > the h-bond cutoff
> specified. --tec3 ""
>
> when its said the bond is there for 96% of the simulation,; what's
> about such low values like 45.5 frmaes and 390 frames? its reallly
> confusing
> would you pls clear it .
What Tom was describing there is a so-called "lifetime" for the hydrogen
bond, which is a measure of how long the hydrogen bond persists once it
is formed during the simulation.
Hydrogen bonds are readily made, broken, and remade during the course of
a simulation. What this measure means is that, on average, this
hydrogen bond (which exists 96% of the simulation), persists for about
45.5 picoseconds (45.5 frames, with each frame being 1 ps apart) before
breaking (and later reforming).
The _longest_ time this hydrogen bond ever lasted was 390 frames (or 390
ps) before breaking (and, again, later reforming).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 07 2014 - 05:30:02 PST
