[gmx-users] Re: g_analyze

[bharat gupta]

I checked the file hbnum.xvg file and it contains three columns - time,
hbonds, hbonds that donot follow the angle criteria. In that case SS1 is
the average of actual hbonds (2nd column ) and SS2 is the average of 3rd
column. Am I right here or not ??

I tried to calculate the h-bond for residues 115-118 individually, and then
checked the average for each residue. For single residue calculation, the
g_analyze average value is correct.

But when I calculate the h-bond as a range 115-118, I get the g_analyze
value as 1.62 . I calculated the average manually in excel, got the average
values as 16.2 [which is (g_analyze avg value)/10].

I then added up the average values of h-bonds of individual residues and
the final comes around 16.2, same as that of the 115-118 range h-bonds.
This means that my calculation is correct.

I also used trjorder to calculate h-bond at distance 0.34 for residues
115-118. I got the average value around 2.51 from g_analyze, where as
manual calculation gives 25.1. I don't knw why for the range the g_analyze
give avg as (actual avg value)/10 ??

Why does trjorder and g_hbond gives different number of hydrogen bonds for
the same residue set??

Thanks
-----------
BHARAT



On Sun, Nov 10, 2013 at 10:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>