[gmx-users] Re: g_analyze

[Justin Lemkul]

On 11/10/13 12:20 AM, bharat gupta wrote:
> 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
>> ..
>
> 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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