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<div>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.</div>
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<div>Sincerely,</div>
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<div>Stephan Watkins</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Freitag, 24. Mai 2013 um 16:04 Uhr<br/>
<b>Von:</b> "Erik Marklund" <erikm@xray.bmc.uu.se><br/>
<b>An:</b> "Discussion list for GROMACS users" <gmx-users@gromacs.org><br/>
<b>Betreff:</b> Re: [gmx-users] the "-dist" flag of g_hbond tool</div>
<div name="quoted-content">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.<br/>
<br/>
Erik<br/>
<br/>
On 24 May 2013, at 15:12, CHEN Pan <evan.pan.chen@gmail.com> wrote:<br/>
<br/>
> Yes. I have looked at it already. I may need to spend time to understand<br/>
> it.<br/>
><br/>
> By the way, in the source code, it seems some part are written for<br/>
> calculating hydrogen bonding energy, but I haven't see any "flag command"<br/>
> could give a output of "hydrogen bonding energy" file. Is it still under<br/>
> development?<br/>
><br/>
><br/>
> 2013/5/24 Erik Marklund <erikm@xray.bmc.uu.se><br/>
><br/>
>> Hm. That is peculiar. The source code has the answer of course. I can have<br/>
>> a look next week to see why that is.<br/>
>><br/>
>> Erik<br/>
>><br/>
>> On 24 May 2013, at 14:11, CHEN Pan <evan.pan.chen@gmail.com> wrote:<br/>
>><br/>
>>> Hi,<br/>
>>><br/>
>>> I have 512 donors and 1024 acceptors.<br/>
>>><br/>
>>> I have just tested "g_hbond" with my standard crystal structure, which I<br/>
>>> should get 512 hydrogen bonds. And the output "hbnum.xvg" does show 512<br/>
>>> hydrogen bonds, which is correct. But the "hbdist.xvg" file still shows<br/>
>>> that the summation of population is 200.<br/>
>>><br/>
>>><br/>
>>> 2013/5/24 Erik Marklund <erikm@xray.bmc.uu.se><br/>
>>><br/>
>>>> Hi,<br/>
>>>><br/>
>>>> See below<br/>
>>>><br/>
>>>> On 24 May 2013, at 11:45, CHEN Pan <evan.pan.chen@gmail.com> wrote:<br/>
>>>><br/>
>>>>> Dear Gromacs users,<br/>
>>>>><br/>
>>>>> I am confused about the g_hbond tools.<br/>
>>>>><br/>
>>>>> 1) When I use "-dist" to get the distribution of hydrogen bonding<br/>
>>>> distance,<br/>
>>>>> I found that the summation of the population is always 200 (the<br/>
>> y-column<br/>
>>>>> below). I am not sure if it's was done with normalization or not, if<br/>
>> yes,<br/>
>>>>> the summation should be one, if no, then the summation should equals to<br/>
>>>> the<br/>
>>>>> total number of the hydrogen bonds, but here the "hbnum.xvg" shows me I<br/>
>>>>> have 440 hydrogen bonds. Why here is always 200, not matter what types<br/>
>> of<br/>
>>>>> hydrogen bonds.<br/>
>>>><br/>
>>>> How many donors do you have, and how many acceptors?<br/>
>>>><br/>
>>>>><br/>
>>>>> 2) In my system, there are several different types of hydrogen bonds,<br/>
>>>> such<br/>
>>>>> as intra-chain and inter-chain or intra-sheet and inter-sheet hydrogen<br/>
>>>>> bonds. Is there any "smart" way to separately calculate those hydrogen<br/>
>>>>> bonds? By using the "index.ndx" file, I could separate the intra-chain<br/>
>>>>> hydrogen bonds, then I can get the inter-chain ones using the total one<br/>
>>>>> minus the intra-chain one. It may be possible to do the same for the<br/>
>>>>> intra-sheet and the inter-sheet. However, this strategy seems<br/>
>> "complex".<br/>
>>>>> Did anybody have experience or ideas for this problem?<br/>
>>>>><br/>
>>>>> Pan<br/>
>>>>><br/>
>>>>> # This file was created Fri May 24 11:06:01 2013<br/>
>>>>> # by the following command:<br/>
>>>>> # g_hbond -f /Users/panchen/gromacs.file/ch1-56/alpha/md-a-re.xtc -s<br/>
>>>>> /Users/panchen/gromacs.file/ch1-56/alpha/md-a.tpr -n ../ful.ndx -b<br/>
>> 11000<br/>
>>>> -e<br/>
>>>>> 16000 -a 30 -r 0.35 -da -num -hbn -ang -dist -g<br/>
>>>>> #<br/>
>>>>> # g_hbond is part of G R O M A C S:<br/>
>>>>> #<br/>
>>>>> # Gromacs Runs One Microsecond At Cannonball Speeds<br/>
>>>>> #<br/>
>>>>> @ title "Hydrogen Bond Distribution"<br/>
>>>>> @ xaxis label "Hydrogen - Acceptor Distance (nm)"<br/>
>>>>> @ yaxis label ""<br/>
>>>>> @TYPE xy<br/>
>>>>> 0.0025 0<br/>
>>>>> 0.0075 0<br/>
>>>>> 0.0125 0<br/>
>>>>> 0.0175 0<br/>
>>>>> 0.0225 0<br/>
>>>>> 0.0275 0<br/>
>>>>> 0.0325 0<br/>
>>>>> 0.0375 0<br/>
>>>>> 0.0425 0<br/>
>>>>> 0.0475 0<br/>
>>>>> 0.0525 0<br/>
>>>>> 0.0575 0<br/>
>>>>> 0.0625 0<br/>
>>>>> 0.0675 0<br/>
>>>>> 0.0725 0<br/>
>>>>> 0.0775 0<br/>
>>>>> 0.0825 0<br/>
>>>>> 0.0875 0<br/>
>>>>> 0.0925 0<br/>
>>>>> 0.0975 0<br/>
>>>>> 0.1025 0<br/>
>>>>> 0.1075 0<br/>
>>>>> 0.1125 0<br/>
>>>>> 0.1175 0<br/>
>>>>> 0.1225 0<br/>
>>>>> 0.1275 0<br/>
>>>>> 0.1325 0<br/>
>>>>> 0.1375 0<br/>
>>>>> 0.1425 0<br/>
>>>>> 0.1475 0<br/>
>>>>> 0.1525 0<br/>
>>>>> 0.1575 0<br/>
>>>>> 0.1625 0<br/>
>>>>> 0.1675 0<br/>
>>>>> 0.1725 0<br/>
>>>>> 0.1775 0<br/>
>>>>> 0.1825 0<br/>
>>>>> 0.1875 0<br/>
>>>>> 0.1925 0<br/>
>>>>> 0.1975 0<br/>
>>>>> 0.2025 0<br/>
>>>>> 0.2075 0<br/>
>>>>> 0.2125 0<br/>
>>>>> 0.2175 0<br/>
>>>>> 0.2225 0<br/>
>>>>> 0.2275 0<br/>
>>>>> 0.2325 0.00538632<br/>
>>>>> 0.2375 0.125501<br/>
>>>>> 0.2425 1.23562<br/>
>>>>> 0.2475 6.08295<br/>
>>>>> 0.2525 16.4279<br/>
>>>>> 0.2575 28.6597<br/>
>>>>> 0.2625 36.0576<br/>
>>>>> 0.2675 35.154<br/>
>>>>> 0.2725 28.1539<br/>
>>>>> 0.2775 19.8073<br/>
>>>>> 0.2825 12.4602<br/>
>>>>> 0.2875 7.23832<br/>
>>>>> 0.2925 4.06577<br/>
>>>>> 0.2975 2.15794<br/>
>>>>> 0.3025 1.14423<br/>
>>>>> 0.3075 0.588366<br/>
>>>>> 0.3125 0.310611<br/>
>>>>> 0.3175 0.163206<br/>
>>>>> 0.3225 0.0772039<br/>
>>>>> 0.3275 0.0411156<br/>
>>>>> 0.3325 0.0210066<br/>
>>>>> 0.3375 0.0113113<br/>
>>>>> 0.3425 0.00574541<br/>
>>>>> 0.3475 0.00502723<br/>
>>>>> --<br/>
>>>>> gmx-users mailing list gmx-users@gromacs.org<br/>
>>>>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br/>
>>>>> * Please search the archive at<br/>
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>>>>> * Please don't post (un)subscribe requests to the list. Use the<br/>
>>>>> www interface or send it to gmx-users-request@gromacs.org.<br/>
>>>>> * Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br/>
>>>><br/>
>>>> --<br/>
>>>> gmx-users mailing list gmx-users@gromacs.org<br/>
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>>>> * Please search the archive at<br/>
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>>>><br/>
>>><br/>
>>><br/>
>>><br/>
>>> --<br/>
>>> Pan Chen<br/>
>>> CERMAV-CNRS<br/>
>>> BP 53<br/>
>>> 38041 Grenoble Cedex 9<br/>
>>> tel. +33 (0)4 76 03 76 12<br/>
>>> fax. +33 (0)4 76 54 72 03<br/>
>>> --<br/>
>>> gmx-users mailing list gmx-users@gromacs.org<br/>
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>>> * Please search the archive at<br/>
>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br/>
>>> * Please don't post (un)subscribe requests to the list. Use the<br/>
>>> www interface or send it to gmx-users-request@gromacs.org.<br/>
>>> * Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br/>
>><br/>
>> --<br/>
>> gmx-users mailing list gmx-users@gromacs.org<br/>
>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br/>
>> * Please search the archive at<br/>
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>> * Please don't post (un)subscribe requests to the list. Use the<br/>
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>><br/>
><br/>
><br/>
><br/>
> --<br/>
> Pan Chen<br/>
> CERMAV-CNRS<br/>
> BP 53<br/>
> 38041 Grenoble Cedex 9<br/>
> tel. +33 (0)4 76 03 76 12<br/>
> fax. +33 (0)4 76 54 72 03<br/>
> --<br/>
> gmx-users mailing list gmx-users@gromacs.org<br/>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br/>
> * Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br/>
> * Please don't post (un)subscribe requests to the list. Use the<br/>
> www interface or send it to gmx-users-request@gromacs.org.<br/>
> * Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br/>
<br/>
--<br/>
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