[gmx-users] the "-dist" flag of g_hbond tool

[Erik Marklund]

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
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