Dear Dr. Cheatham,
I'm very sorry for my delayed response, and thank you very much for your
detailed reply.
Kamali
On Fri, May 6, 2011 at 5:12 PM, Thomas Cheatham III <tec3.utah.edu> wrote:
>
> > 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 Mon Aug 01 2011 - 05:00:03 PDT
