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

[CHEN Pan]

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
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