g_hbond(1)

NAME

g_hbond - computes and analyzes hydrogen bonds

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  -don donor.xvg -dan
danum.xvg -life hblife.xvg -[no]h -nice int -b time -e  time  -dt  time
-[no]xvgr  -[no]ins  -a  real  -r  real  -[no]da  -abin real -rbin real
-[no]nitacc -[no]contact -shell real -fitstart real  -temp  real  -dump
int  -max_hb  real -[no]merge -acflen int -[no]normalize -P enum -fitfn
enum -ncskip int -beginfit real -endfit real

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 . 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.

It is also possible to analyse specific hydrogen bonds with

-sel . This index file must contain a group of atom triplets 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; 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: 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
-don donor.xvg Output, Opt.: xvgr/xmgr file
-dan danum.xvg Output, Opt.: xvgr/xmgr file
-life hblife.xvg Output, Opt.: xvgr/xmgr file

OTHER OPTIONS

-[no]h no: Print help info and quit
-nice int 19: Set the nicelevel
-b time 0: First frame (ps) to read from trajectory
-e time 0: Last frame (ps) to read from trajectory
-dt time 0: Only use frame when t MOD dt = first time (ps)
-[no]xvgr yes: Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-[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
-fitstart real 1: Time from which to start fitting the correlation functions in order to
obtain the forward and backward rate constants for HB breaking and formation
-temp real 298.15: Temperature (K) for computing the Gibbs energy corresponding to HB
breaking and reforming
-dump int 0: Dump the first N hydrogen bond ACFs 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 acceptor, but with different hydro
gen are treated as a single H-bond. Mainly important for the ACF.
-acflen int -1: Length of the ACF, default is half the number of frames
-[no]normalize yes: Normalize ACF
-P enum 0: Order of Legendre polynomial for ACF (0 indicates none): 0 , 1 , 2 or
3
-fitfn enum none: Fit function: none , exp , aexp , exp_exp , vac , exp5 , exp7 or exp9
-ncskip int 0: Skip N points in the output file of correlation functions
-beginfit real 0: Time where to begin the exponential fit of the correlation function
-endfit real -1: Time where to end the exponential fit of the correlation function, -1
is till the end

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