> I'm trying to understand the schematic that the latest version of ptraj
> gives in its hydrogen bonding facility:
>
> I understand that this is the key for what the symbols mean:
>
> * Dumping schematic of time series after each h-bond, key follows:
> | . - o x * . |
> 0-5% 5-20% 20-40% 40-60% 60-80% 80-95% 95-100% occupancy*
>
> My question is: %occupancy of what? I've used the H-bonding facility to
How often the h-bond is formed as a percentage...
> analyze trajectories both 100ns and 20ns long, and both times I've seen a
> string of 50 symbols to the right of the output table. What would one string
> represent? For example:
>
> *| ..-.o.- .---. o.. o..................x *....o.|*
Each symbol represents the %time the h-bond is formed for "total
trajectory" / 50. So, in the first part of the trajectory, the h-bond is
not or only partially formed, then later it is mostly formed...
> What does it mean to say that, for each ".", the H-bond is 95-100% occupied
> for 1/50 of the trajectory? Does this mean, if I specified my cutoff
> distance as 4 and my angle as 179, that the Hbond form at 1/50 of the
> trajectory was at least (0.95)*4 = 3.8 Å in length and at an angle of at
> least 179.95º?
No, it means that over that 1/50 time interval, > 95% of the time the bond
was less than 4.0 A. To get an idea of the average h-bond length (while
< 4.0 A) see the average bond length printed.
--tec3
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Received on Fri May 06 2011 - 14:30:03 PDT
