erikm at xray.bmc.uu.se
Fri May 24 09:42:26 CEST 2013
Just to clarify: The third column are the number of acceptor-donor pairs that fulfil the distance criterion but not the angle criterion.
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.
> 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 !
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