[gmx-users] the "-dist" flag of g_hbond tool
CHEN Pan
evan.pan.chen at gmail.com
Fri May 24 15:12:09 CEST 2013
Yes. I have looked at it already. I may need to spend time to understand
it.
By the way, in the source code, it seems some part are written for
calculating hydrogen bonding energy, but I haven't see any "flag command"
could give a output of "hydrogen bonding energy" file. Is it still under
development?
2013/5/24 Erik Marklund <erikm at xray.bmc.uu.se>
> 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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> >>
> >> --
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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
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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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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