[gmx-users] g_hbond

[Erik Marklund]

Hi,

Just to clarify: The third column are the number of acceptor-donor pairs that fulfil the distance criterion but not the angle criterion.

Erik

On 24 May 2013, at 09:06, CHEN Pan <evan.pan.chen at gmail.com> wrote:

> Hi Maggin,
> The middle column is the total number of hydrogen bonds in your system
> under the definition of the hydrogen bonds criteria you have defined (here
> you used the default value). The third column is the number of
> acceptor-donor paris in the system. The first column is the simulation
> time, your trajectory file are saved every 2 ps right?
> If you use "xmgrace bovin_hnum.xvg", you can easily find what's the meaning
> of the second and third column.
> 
> Pan
> 
> 2013/5/24 maggin <maggin.chen at gmail.com>
> 
>> # This file was created Fri May 24 13:03:14 2013
>> # by the following command:
>> # g_hbond -f traj_all_md.trr -s md_0_1_next1.tpr -num bovin_hnum.xvg
>> #
>> # g_hbond is part of G R O M A C S:
>> #
>> # Green Red Orange Magenta Azure Cyan Skyblue
>> #
>> @    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"
>>         0          74         517
>>         2          73         515
>>         4          69         515
>>         6          69         529
>>         8          78         525
>>        10          74         517
>>        12          68         516
>>        14          68         524
>>        16          71         520
>>       ........
>> hi, anybody can tell me at here if Hydrogen bonds Refers to the middle
>> column: 74,73,69,69,78,74,68,68,71
>> 
>> Thank you !
>> 
>> maggin
>> 
>> 
>> 
>> 
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