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