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

Erik Marklund erikm at xray.bmc.uu.se
Fri May 24 16:04:44 CEST 2013 

It used to be. I didn't realise it was still in the code. We experimented a bit with having a continuous bond criterion instead of a binary measure. It didn't do for us what we hoped it would so it was abandoned. I know that some people are using Espiniozas empirical formula for bond energy, however, so that code may be resurrected at some point.

Erik

On 24 May 2013, at 15:12, CHEN Pan <evan.pan.chen at gmail.com> wrote:

> 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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>>> 
>>> 
>>> 
>>> --
>>> 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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>> 
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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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