g_hbond (1) - Linux Manuals
g_hbond: computes and analyzes hydrogen bonds
NAMEg_hbond - computes and analyzes hydrogen bonds
SYNOPSISg_hbond -f traj.xtc -s topol.tpr -n index.ndx -num hbnum.xvg -g hbond.log -ac hbac.xvg -dist hbdist.xvg -ang hbang.xvg -hx hbhelix.xvg -hbn hbond.ndx -hbm hbmap.xpm -don donor.xvg -dan danum.xvg -life hblife.xvg -nhbdist nhbdist.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr -[no]ins -a real -r real -[no]da -r2 real -abin real -rbin real -[no]nitacc -[no]contact -shell real -fitstart real -temp real -smooth real -dump int -max_hb real -[no]merge -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real
DESCRIPTIONg_hbond computes and analyzes hydrogen bonds. Hydrogen bonds are determined based on cutoffs for the angle Acceptor - Donor - Hydrogen (zero is extended) and the distance Hydrogen - Acceptor. OH and NH groups are regarded as donors, O is an acceptor always, N is an acceptor by default, but this can be switched using -nitacc. Dummy hydrogen atoms are assumed to be connected to the first preceding non-hydrogen atom.
You need to specify two groups for analysis, which must be either identical or non-overlapping. All hydrogen bonds between the two groups are analyzed.
If you set -shell, you will be asked for an additional index group which should contain exactly one atom. In this case, only hydrogen bonds between atoms within the shell distance from the one atom are considered.
[ selected ]
20 21 24
25 26 29
1 3 6
Note that the triplets need not be on separate lines. Each atom triplet specifies a hydrogen bond to be analyzed, note also that no check is made for the types of atoms.
-ins turns on computing solvent insertion into hydrogen bonds. In this case an additional group must be selected, specifying the solvent molecules.
-num: number of hydrogen bonds as a function of time.
-ac: average over all autocorrelations of the existence functions (either 0 or 1) of all hydrogen bonds.
-dist: distance distribution of all hydrogen bonds.
-ang: angle distribution of all hydrogen bonds.
-hx: the number of n-n+i hydrogen bonds as a function of time where n and n+i stand for residue numbers and i ranges from 0 to 6. This includes the n-n+3, n-n+4 and n-n+5 hydrogen bonds associated with helices in proteins.
-hbn: all selected groups, donors, hydrogens and acceptors for selected groups, all hydrogen bonded atoms from all groups and all solvent atoms involved in insertion.
-hbm: existence matrix for all hydrogen bonds over all frames, this also contains information on solvent insertion into hydrogen bonds. Ordering is identical to that in -hbn index file.
-dan: write out the number of donors and acceptors analyzed for each timeframe. This is especially usefull when using -shell.
-nhbdist: compute the number of HBonds per hydrogen in order to compare results to Raman Spectroscopy.
Note: options -ac, -life, -hbn and -hbm require an amount of memory proportional to the total numbers of donors times the total number of acceptors in the selected group(s).
FILES-f traj.xtc Input
-nice int 19
-b time 0
-e time 0
-dt time 0
-a real 30
-r real 0.35
-r2 real 0
-abin real 1
-rbin real 0.005
-shell real -1
-fitstart real 1
-temp real 298.15
-smooth real -1
-dump int 0
-max_hb real 0
-acflen int -1
-P enum 0
-fitfn enum none
-ncskip int 0
-beginfit real 0
-endfit real -1
KNOWN PROBLEMS- The option -sel that used to work on selected hbonds is out of order, and therefore not available for the time being.
More information about GROMACS is available at <http://www.gromacs.org/>.