Re: [AMBER] H-bond analysis interpratation

From: Thomas Cheatham III <tec3.utah.edu>
Date: Wed, 5 Jan 2011 13:10:57 -0700 (Mountain Standard Time)

> Here I want to know one more thing what is the default value of time, Is it 1 ?

The default value is 1.0 * [the spacing between frames]. If the spacing
between frames is 5 ns, then you will only get data every 5 ns. If you
dump every ps, then the time is 1 ps.

>
> In Amber tutorial:- http://ambermd.org/tutorials/basic/tutorial3/section6.htm
>
> Occupancy of H-bonding (last column)is define in form of time of MD run i.e.
> percentage occupency is written after every 5ns of trajectory.
>
> Is it possible in amber11 to get such form of result ?

AmberTools prints out a larger number of "points" (50) for this pseudo
h-bond time course plot...


| 292 :10.O5' | 287 :9.HO'2 286 :9.O2' | 24.30 3.079 ( 0.22) 39.59 (12.43) 2.4 ( 6.6) 109
|---.--.-....-o.@@o.....--.-......-....--.--.--...-|

Therefore the spacing in this plot is effectively the (total number of
frames read in) / 50. To alter this behavior would require code changes.

--tec3


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Received on Wed Jan 05 2011 - 12:30:02 PST
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