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
