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

[Erik Marklund]

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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