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

[CHEN Pan]

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.

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