> 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
