table of contents
g_hbond(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_hbond(1) |
NAME¶
g_hbond - computes and analyzes hydrogen bondsSYNOPSIS¶
g_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 -[no]version -nice int -b time -e time -dt time -tu enum -xvg enum -a real -r real -[no]da -r2 real -abin real -rbin real -[no]nitacc -[no]contact -shell real -fitstart real -fitstart real -temp real -smooth real -dump int -max_hb real -[no]merge -geminate enum -diff real -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit realDESCRIPTION¶
g_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.FILES¶
-f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt
Run input file: tpr tpb tpa
Index file
xvgr/xmgr file
Log file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
Index file
X PixMap compatible matrix file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
Time unit: fs, ps, ns, us, ms or s
xvg plot formatting: xmgrace, xmgr or none
Cutoff angle (degrees, Acceptor - Donor - Hydrogen)
Cutoff radius (nm, X - Acceptor, see next option)
Use distance Donor-Acceptor (if TRUE) or Hydrogen-Acceptor (FALSE)
Second cutoff radius. Mainly useful with -contact and -ac
Binwidth angle distribution (degrees)
Binwidth distance distribution (nm)
Regard nitrogen atoms as acceptors
Do not look for hydrogen bonds, but merely for contacts within the cut-off distance
when 0, only calculate hydrogen bonds within nm shell around one particle
Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation. With -gemfit we suggest -fitstart 0
Time (ps) to which to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation (only with -gemfit)
Temperature (K) for computing the Gibbs energy corresponding to HB breaking and reforming
If = 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/tau)
Dump the first N hydrogen bond ACFs in a single .xvg file for debugging
Theoretical maximum number of hydrogen bonds used for normalizing HB autocorrelation function. Can be useful in case the program estimates it wrongly
H-bonds between the same donor and acceptor, but with different hydrogen are treated as a single H-bond. Mainly important for the ACF.
Use reversible geminate recombination for the kinetics/thermodynamics calclations. See Markovitch et al., J. Chem. Phys 129, 084505 (2008) for details.: none, dd, ad, aa or a4
Dffusion coefficient to use in the reversible geminate recombination kinetic model. If negative, then it will be fitted to the ACF along with ka and kd.
Length of the ACF, default is half the number of frames
Normalize ACF
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9 or erffit
Skip N points in the output file of correlation functions
Time where to begin the exponential fit of the correlation function
Time where to end the exponential fit of the correlation function, -1 is until the end
KNOWN PROBLEMS¶
- The option -sel that used to work on selected hbonds is out of order, and therefore not available for the time being.SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |