just want to add to Dan's comment.
If you (Hadeer) know about Python, you can use pytraj (python front end of
cpptraj) to gain more control to cpptraj without update C++ code.
I have a tutorial here relating to hbond with some statistics:
http://amber-md.github.io/pytraj/latest/tutorials/plot_hbond_basic.html
The main idea is similar to Dan's comment
+ use pytraj's hbond to call cpptraj calculation to get a series of makes
(distance and angle maskes)
+ compute distance and angle for all given makes
+ do the filtering to get only distances and angles that form hbond
+ use numpy to do stat
sounds complicated but all are in above tutorial. (But in the future, both
cpptraj/pytraj will definitely have ready-to-used data)
Hope this help
Hai
On Mon, Dec 7, 2015 at 11:04 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Sun, Dec 6, 2015 at 8:20 AM, Hadeer ELHabashy
> <hadeer.elhabashi.gmail.com> wrote:
> > Is it possible to calculate the standard deviation of the Hydrogen
> bonding
> > 's lengths and angles directly using the Hbond command ?!
>
> It's certainly possible, but currently not straightforward. This data
> is currently not stored by the 'hbond' command. What you would
> currently have to do is save the hydrogen bond time series data (using
> the "series" keyword), read that data back in, then use a combination
> of the 'filter' command with the 'hbond' series data followed by the
> 'distance'/'angle' commands to calculate the raw distance and angle
> values when the hydrogen bond is present, and lastly calculate your
> average/stdev from those values (using e.g. the 'avg' analysis
> command). The problem is you would have to do this for *each* hydrogen
> bond separately, which is going to be pretty slow.
>
> This is certainly something I can consider adding to cpptraj 'hbond'
> output at some point.
>
> -Dan
>
> PS - If you have any programming experience, it may be easier to e.g.
> modify the HbondType structure in Action_Hbond.cpp to hold the sum of
> squared distances/angles for the purpose of calculating the standard
> deviation yourself.
>
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Mon Dec 07 2015 - 12:30:04 PST
