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 -- 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
