The hydrogen bonding energy would have/is usefull to myself. An example, I use the .ndx as you did below for protein-protein interactions only. I get around 25 and 28 for two different states. The interesting part is the 25 is about 7 times the delG, however the hydrogen bonds move much less, and remain in contact longer across the trajectory. A nice hydrogen bonding energy (real Vs. Calculated) would have added a nice graph to make a point.
Sincerely,
Stephan Watkins
Gesendet: Freitag, 24. Mai 2013 um 16:04 Uhr
Von: "Erik Marklund" <er...@xray.bmc.uu.se>
An: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Betreff: Re: [gmx-users] the "-dist" flag of g_hbond tool
Von: "Erik Marklund" <er...@xray.bmc.uu.se>
An: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Betreff: Re: [gmx-users] the "-dist" flag of g_hbond tool
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.c...@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 <er...@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.c...@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 <er...@xray.bmc.uu.se>
>>>
>>>> Hi,
>>>>
>>>> See below
>>>>
>>>> On 24 May 2013, at 11:45, CHEN Pan <evan.pan.c...@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
>>>>> --
>>>>> gmx-users mailing list gmx-users@gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>> * Please don't post (un)subscribe requests to the list. Use the
>>>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> --
>>>> gmx-users mailing list gmx-users@gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> * Please don't post (un)subscribe requests to the list. Use the
>>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>
>>>
>>>
>>> --
>>> 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@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> --
>> gmx-users mailing list gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> 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@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
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Erik
On 24 May 2013, at 15:12, CHEN Pan <evan.pan.c...@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 <er...@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.c...@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 <er...@xray.bmc.uu.se>
>>>
>>>> Hi,
>>>>
>>>> See below
>>>>
>>>> On 24 May 2013, at 11:45, CHEN Pan <evan.pan.c...@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
>>>>> --
>>>>> gmx-users mailing list gmx-users@gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>> * Please don't post (un)subscribe requests to the list. Use the
>>>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> --
>>>> gmx-users mailing list gmx-users@gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> * Please don't post (un)subscribe requests to the list. Use the
>>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>
>>>
>>>
>>> --
>>> 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@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> --
>> gmx-users mailing list gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> 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@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
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