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. 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