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
