Re: [gmx-users] Re: g_analyze

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On 11/10/13 12:20 AM, bharat gupta wrote:
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```Hi,
I used the command g_hbond to find h-bond between  residues 115-118 and
water. Then I used g_analyze to find out the average and it gives the value
for the hbonds like this :-

std. dev.    relative deviation of
standard       ---------   cumulants from those of
set      average       deviation      sqrt(n-1)   a Gaussian distribition
cum. 3   cum. 4
SS1   6.877249e-02   2.546419e-01   5.092839e-03       2.181    3.495
SS2   6.997201e-02   2.673450e-01   5.346901e-03       2.421    5.001

When I calculated the average manually, by taking the average of numbers in
second column of hbnum.xvg file, I got a value of around 13.5.. What is the
reason for such a large difference.

```
```
```
Hard to say, but I've never known g_analyze to be wrong, so I'd suspect something is amiss in your manual calculation. The difference between 13.5 and 0.0069 is huge; you should be able to scan through the data file to see what the expected value should be.
```
```
```In another case, g_analyze gives avg values of aroun 6.9 for hbond between
two residues and when I calculated it maually I got the avg values as 6.8
```
```..
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```
Whats the meaning of SS1 and SS2,?? Does it mean that SS1 refers to time
and SS2 refers to hbond numbers in the hbnum.xvg obtained from g_hbond
analysis ??
```
```
```
Data sets 1 and 2. You will note that there are two columns of data in the -hbnum output produced by g_hbond, with titles explaining both.
```
-Justin

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

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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