On 11/10/13 8:38 PM, bharat gupta wrote:
But trjorder can be used to calculate the hydration layer or shell around
residues ... Right ??
Yes, but I also tend to think that integrating an RDF is also a more
straightforward way of doing that. With trjorder, you set some arbitrary cutoff
that may or may not be an informed decision - with an RDF it is clear where the
hydration layers are.
-Justin
On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 11/10/13 8:30 PM, bharat gupta wrote:
Thanks for your reply. I was missing the scientific notation part. Now
everything is fine.
Regarding trjorder, it doesn't measure h-bonds but gives the water nearest
to protein.
I wouldn't try to draw any sort of comparison between the output of
trjorder and g_hbond. If you want to measure H-bonds, there's only one
tool for that.
-Justin
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