[gmx-users] the "-dist" flag of g_hbond tool
Erik Marklund
erikm at xray.bmc.uu.se
Fri May 24 15:06:49 CEST 2013
Hm. That is peculiar. The source code has the answer of course. I can have a look next week to see why that is.
Erik
On 24 May 2013, at 14:11, CHEN Pan <evan.pan.chen at gmail.com> wrote:
> Hi,
>
> I have 512 donors and 1024 acceptors.
>
> I have just tested "g_hbond" with my standard crystal structure, which I
> should get 512 hydrogen bonds. And the output "hbnum.xvg" does show 512
> hydrogen bonds, which is correct. But the "hbdist.xvg" file still shows
> that the summation of population is 200.
>
>
> 2013/5/24 Erik Marklund <erikm at xray.bmc.uu.se>
>
>> Hi,
>>
>> See below
>>
>> On 24 May 2013, at 11:45, CHEN Pan <evan.pan.chen at gmail.com> wrote:
>>
>>> Dear Gromacs users,
>>>
>>> I am confused about the g_hbond tools.
>>>
>>> 1) When I use "-dist" to get the distribution of hydrogen bonding
>> distance,
>>> I found that the summation of the population is always 200 (the y-column
>>> below). I am not sure if it's was done with normalization or not, if yes,
>>> the summation should be one, if no, then the summation should equals to
>> the
>>> total number of the hydrogen bonds, but here the "hbnum.xvg" shows me I
>>> have 440 hydrogen bonds. Why here is always 200, not matter what types of
>>> hydrogen bonds.
>>
>> How many donors do you have, and how many acceptors?
>>
>>>
>>> 2) In my system, there are several different types of hydrogen bonds,
>> such
>>> as intra-chain and inter-chain or intra-sheet and inter-sheet hydrogen
>>> bonds. Is there any "smart" way to separately calculate those hydrogen
>>> bonds? By using the "index.ndx" file, I could separate the intra-chain
>>> hydrogen bonds, then I can get the inter-chain ones using the total one
>>> minus the intra-chain one. It may be possible to do the same for the
>>> intra-sheet and the inter-sheet. However, this strategy seems "complex".
>>> Did anybody have experience or ideas for this problem?
>>>
>>> Pan
>>>
>>> # This file was created Fri May 24 11:06:01 2013
>>> # by the following command:
>>> # g_hbond -f /Users/panchen/gromacs.file/ch1-56/alpha/md-a-re.xtc -s
>>> /Users/panchen/gromacs.file/ch1-56/alpha/md-a.tpr -n ../ful.ndx -b 11000
>> -e
>>> 16000 -a 30 -r 0.35 -da -num -hbn -ang -dist -g
>>> #
>>> # g_hbond is part of G R O M A C S:
>>> #
>>> # Gromacs Runs One Microsecond At Cannonball Speeds
>>> #
>>> @ title "Hydrogen Bond Distribution"
>>> @ xaxis label "Hydrogen - Acceptor Distance (nm)"
>>> @ yaxis label ""
>>> @TYPE xy
>>> 0.0025 0
>>> 0.0075 0
>>> 0.0125 0
>>> 0.0175 0
>>> 0.0225 0
>>> 0.0275 0
>>> 0.0325 0
>>> 0.0375 0
>>> 0.0425 0
>>> 0.0475 0
>>> 0.0525 0
>>> 0.0575 0
>>> 0.0625 0
>>> 0.0675 0
>>> 0.0725 0
>>> 0.0775 0
>>> 0.0825 0
>>> 0.0875 0
>>> 0.0925 0
>>> 0.0975 0
>>> 0.1025 0
>>> 0.1075 0
>>> 0.1125 0
>>> 0.1175 0
>>> 0.1225 0
>>> 0.1275 0
>>> 0.1325 0
>>> 0.1375 0
>>> 0.1425 0
>>> 0.1475 0
>>> 0.1525 0
>>> 0.1575 0
>>> 0.1625 0
>>> 0.1675 0
>>> 0.1725 0
>>> 0.1775 0
>>> 0.1825 0
>>> 0.1875 0
>>> 0.1925 0
>>> 0.1975 0
>>> 0.2025 0
>>> 0.2075 0
>>> 0.2125 0
>>> 0.2175 0
>>> 0.2225 0
>>> 0.2275 0
>>> 0.2325 0.00538632
>>> 0.2375 0.125501
>>> 0.2425 1.23562
>>> 0.2475 6.08295
>>> 0.2525 16.4279
>>> 0.2575 28.6597
>>> 0.2625 36.0576
>>> 0.2675 35.154
>>> 0.2725 28.1539
>>> 0.2775 19.8073
>>> 0.2825 12.4602
>>> 0.2875 7.23832
>>> 0.2925 4.06577
>>> 0.2975 2.15794
>>> 0.3025 1.14423
>>> 0.3075 0.588366
>>> 0.3125 0.310611
>>> 0.3175 0.163206
>>> 0.3225 0.0772039
>>> 0.3275 0.0411156
>>> 0.3325 0.0210066
>>> 0.3375 0.0113113
>>> 0.3425 0.00574541
>>> 0.3475 0.00502723
>>> --
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>
>
>
> --
> Pan Chen
> CERMAV-CNRS
> BP 53
> 38041 Grenoble Cedex 9
> tel. +33 (0)4 76 03 76 12
> fax. +33 (0)4 76 54 72 03
> --
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