Re: [gmx-users] Re: g_analyze

```
On 11/11/13 5:39 PM, bharat gupta wrote:
```
```Sorry, I attached the wrong file . Here's the average file generate from
one of the files I sent in my last mail. I used the command g_analyze -f
hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained
from this command :-

https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water-avg.xvg

Now, if you see, the graph (in previous mail) and average file, both
correlates well. I have a doubt about interpreting the result from
g_analyze. The value "7.150740e+00" implies that on average 7 hydrogen
bonds are formed during the simulation time of 5ns to 10ns. What does then
the average file or its graph tells ??

```
```
```
It's an average over sets. It is not equivalent to the output printed to the screen, nor is it supposed to. The value printed to the screen is the actual average of the data set of interest, as is intuitive from your values. An average of 4 is impossible if all the data points are in the range of 6-9.
```
-Justin

```
```

On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul <jalem...@vt.edu> wrote:

```
```

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

-Justin

```
```On Mon, Nov 11, 2013 at 3:30 PM, bharat gupta <bharat.85.m...@gmail.com>
wrote:

```
```
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:

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

--
==================================================

Justin A. Lemkul, Ph.D.
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Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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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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==================================================

Justin A. Lemkul, Ph.D.
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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==================================================

Justin A. Lemkul, Ph.D.
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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