[gmx-users] Re: g_analyze

[bharat gupta]

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.




On Mon, Nov 11, 2013 at 10:12 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/10/13 7:18 PM, bharat gupta wrote:
>
>> 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 third column is not actually H-bonds, then ;)
>
>
>  the average of actual hbonds (2nd column ) and SS2 is the average of 3rd
>> column. Am I right here or not ??
>>
>>
> Yes.
>
>
>  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].
>>
>>
> That is impossible.  You cannot get a different average by examining the
> same numbers.  Read the g_analyze output again - I am willing to bet that
> you're not seeing the exponent of the scientific notation.
>
>
>  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??
>>
>>
> All of this comes down to correctly reading the screen output.  I have no
> idea what you're doing with trjorder, though.  It doesn't measure H-bonds.
>
>
> -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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