On 11/11/13 4:06 AM, bharat gupta wrote:
In addition to my previous question, I have another question about
g_analyze. When I used the hbond.xvg file to get the average and plotted
the average.xvg file I found that the average value is round 4 to 5
according to the graph. But g_analyze in its final calculation gives 7.150
as the average values... Here's the link for the graph and result of
average value calculated by g_analyze :-
std. dev. relative deviation of
standard --------- cumulants from those of
set average deviation sqrt(n-1) a Gaussian distribition
cum. 3 cum. 4
SS1 * 7.150740e+00 * 8.803173e-01 1.760635e-02 0.062 0.163
SS2 1.490604e+00 1.164761e+00 2.329523e-02 0.495 0.153
https://www.dropbox.com/s/1vqixenyerha7qq/115-water.png
Here's the link hbond.xvg file and its averaged file
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
https://www.dropbox.com/s/4n0m47o3mrjn3o8/hbond_115-water.xvg
Neither of these files produce output that corresponds to the PNG image above.
Both files have values in 6-9 H-bond range and thus agree with the g_analyze
output, which I can reproduce. I suspect you're somehow getting your files
mixed up.
-Justin
On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta <bharat.85.m...@gmail.com>wrote:
thank you informing about g_rdf...
Is it possible to dump the structure with those average water molecules
interacting with the residues. I generated the hbond.log file which gives
the details but I need to generate a figure for this ??
On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul <jalem...@vt.edu> wrote:
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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Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
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jalem...@outerbanks.umaryland.edu | (410) 706-7441
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Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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