[gmx-users] DETECTING HYDROGEN BONDS

[jkrieger at mrc-lmb.cam.ac.uk]

I think the 2nd column is the number of hydrogen bonds based on distance
and angle whereas the 3rd column is all pairs within the 0.35 nm distance
cutoff ignoring angles. This is stated by the lines

@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"

Best wishes
James

> Thank you very much for the reply
>
>
> Wanted to know what the third column represents?
>
>
> The header was
>
>
> # gmx hbond is part of G R O M A C S:
> # # Glycine aRginine prOline Methionine Alanine Cystine Serine #
> @    title "Hydrogen Bonds"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "Number"
> @TYPE xy @ view 0.15, 0.15, 0.75, 0.85
> @ legend on @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "Hydrogen bonds"
> @ s1 legend "Pairs within 0.35 nm"
>
> Through molecular docking had obtained hydrogen bonding with GLU 387 AND
> GLU 389
>
> Wish to ascertain them through simulations too. How to do it?
>
> Thanks,
> Subashini.K
>
>
>
>
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Alex
> <nedomacho at gmail.com>
> Sent: Saturday, February 11, 2017 1:45 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] DETECTING HYDROGEN BONDS
>
> Not sure what you mean by "interpret these numbers," except that now we
> know that your simulation was 2 ns long.  The xvg file contains a
> header, which describes what each column is. If I recall correctly, the
> second column is the number of hbonds according to the default search
> cutoff. The first column is your simulated time in ps.
>
> Alex
>
>
> On 2/11/2017 1:00 AM, Subashini .K wrote:
>> Hi gromacs users,
>>
>>
>> After protein ligand simulations, gave the following command to detect
>> hydrogen bond
>>
>>
>> gmx hbond -f npt.trr -s npt.tpr -num hbond.xvg
>>
>> After selecting protein and ligand
>>
>>
>> Obtained the following result
>>
>>
>> I am a beginner. Could someone help me  to interpret these numbers? The
>> simulation was done for 2 ns
>>
>>
>>
>>                  0           2           1
>>
>>                100           2           1
>>
>>                 200           1           0
>>
>>                 300           1           0
>>
>>                 400           1           0
>>
>>                 500           1           0
>>
>>                 600           1           0
>>
>>                700           1           0
>>
>>                800           0           0
>>
>>                900           1           0
>>
>>             1000           1           0
>>
>>              1100           1           0
>>
>>           1200           1           0
>>
>>           1300           0           2
>>
>>          1400           1           0
>>
>>           1500           1           0
>>
>>           1600           1           0
>>
>>            1700           1           0
>>
>>           1800           0           1
>>
>>            1900           1           0
>>
>>           2000           1           0
>>
>>
>> Thanks,
>>
>> Subashini.K
>
>
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