g_hbond(1)

NAME
g_hbond VERSION 3.2.0

SYNOPSIS
g_hbond -f traj.xtc -s topol.tpr -n index.ndx -g hbond.log -sel select.ndx -num hbnum.xvg -ac hbac.xvg -dist hbdist.xvg -ang hbang.xvg -hx hbhelix.xvg -hbn hbond.ndx -hbm hbmap.xpm -dan danum.xvg -[no]h -nice int -b time -e time -dt time -[no]ins -a real -r real -[no]da -abin real -rbin real -[no]nitacc -[no]contact -shell real -[no]dump -max_hb real -[no]merge

DESCRIPTION
g_hbond computes and analyzes hydrogen bonds. Hydrogen bonds are determined based on cutoffs for the angle Donor - Hydrogen - Acceptor (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 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. It is also possible to analyse specific hydrogen bonds with -sel Donor Hydrogen Acceptor, in the following way: [ 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. Output: -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

FILES
-f traj.xtc Input
 Generic trajectory: xtc trr trj gro g96 pdb -s topol.tpr Input
 Generic run input: tpr tpb tpa xml -n index.ndx Input, Opt.
 Index file -g hbond.log Output, Opt.
 Log file -sel select.ndx Input, Opt.
 Index file -num hbnum.xvg Output
 xvgr/xmgr file -ac hbac.xvg Output, Opt.
 xvgr/xmgr file -dist hbdist.xvg Output, Opt.
 xvgr/xmgr file -ang hbang.xvg Output, Opt.
 xvgr/xmgr file -hx hbhelix.xvg Output, Opt.
 xvgr/xmgr file -hbn hbond.ndx Output, Opt.
 Index file -hbm hbmap.xpm Output, Opt.
 X PixMap compatible matrix file -dan danum.xvg Output, Opt.
 xvgr/xmgr file

OTHER OPTIONS
-[no]h no
 Print help info and quit -nice int 19
 Set the nicelevel -b time -1
 First frame (ps) to read from trajectory -e time -1
 Last frame (ps) to read from trajectory -dt time -1
 Only use frame when t MOD dt = first time (ps) -[no]ins no
 Analyze solvent insertion -a real 30
 Cutoff angle (degrees, Donor - Hydrogen - Acceptor) -r real 0.35
 Cutoff radius (nm, X - Acceptor, see next option) -[no]da yes
 Use distance Donor-Acceptor (if TRUE) or Hydrogen-Acceptor (FALSE) -abin real 1
 Binwidth angle distribution (degrees) -rbin real 0.005
 Binwidth distance distribution (nm) -[no]nitacc yes
 Regard nitrogen atoms as acceptors -[no]contact no
 Do not look for hydrogen bonds, but merely for contacts within the cut-off distance -shell real -1
 when 0, only calculate hydrogen bonds within nm shell around one particle -[no]dump no
 Dump all hydrogen bond ACFs (maximum 1000) in a single xvg file for debugging -max_hb real 0
 Theoretical maximum number of hydrogen bonds used for normalizing HB autocorrelation function. Can be useful in case the program estimates it wrongly -[no]merge yes
 H-bonds between the same donor and accepter, but with different hydrogen are treated as a single H-bond. Mainly important for the ACF.