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本帖最后由 Graphite 于 2024-6-23 11:51 编辑
RTFM
:-) GROMACS - gmx hbond, 2023.2 (-:
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /mnt/d/
Command line:
gmx hbond -h
SYNOPSIS
gmx hbond [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-n [<.ndx>]] [-num [<.xvg>]]
[-g [<.log>]] [-ac [<.xvg>]] [-dist [<.xvg>]] [-ang [<.xvg>]]
[-hx [<.xvg>]] [-hbn [<.ndx>]] [-hbm [<.xpm>]] [-don [<.xvg>]]
[-dan [<.xvg>]] [-life [<.xvg>]] [-nhbdist [<.xvg>]] [-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>]
[-fitend <real>] [-temp <real>] [-dump <int>] [-max_hb <real>]
[-[no]merge] [-nthreads <int>] [-acflen <int>] [-[no]normalize]
[-P <enum>] [-fitfn <enum>] [-beginfit <real>] [-endfit <real>]
DESCRIPTION
gmx hbond computes and analyzes hydrogen bonds. Hydrogen bonds are determined
based on cutoffs for the angle Hydrogen - Donor - Acceptor (zero is extended)
and the distance Donor - Acceptor (or Hydrogen - Acceptor using -noda). 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.
With option -ac, rate constants for hydrogen bonding can be derived with the
model of Luzar and Chandler (Nature 379:55, 1996; J. Chem. Phys. 113:23,
2000). If contact kinetics are analyzed by using the -contact option, then
n(t) can be defined as either all pairs that are not within contact distance r
at time t (corresponding to leaving the -r2 option at the default value 0) or
all pairs that are within distance r2 (corresponding to setting a second
cut-off value with option -r2). See mentioned literature for more details and
definitions.
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. Output is limited unless -nomerge is set.
* -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 useful 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).
OPTIONS
Options to specify input files:
-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
-s [<.tpr>] (topol.tpr)
Portable xdr run input file
-n [<.ndx>] (index.ndx) (Opt.)
Index file
Options to specify output files:
-num [<.xvg>] (hbnum.xvg)
xvgr/xmgr file
-g [<.log>] (hbond.log) (Opt.)
Log file
-ac [<.xvg>] (hbac.xvg) (Opt.)
xvgr/xmgr file
-dist [<.xvg>] (hbdist.xvg) (Opt.)
xvgr/xmgr file
-ang [<.xvg>] (hbang.xvg) (Opt.)
xvgr/xmgr file
-hx [<.xvg>] (hbhelix.xvg) (Opt.)
xvgr/xmgr file
-hbn [<.ndx>] (hbond.ndx) (Opt.)
Index file
-hbm [<.xpm>] (hbmap.xpm) (Opt.)
X PixMap compatible matrix file
-don [<.xvg>] (donor.xvg) (Opt.)
xvgr/xmgr file
-dan [<.xvg>] (danum.xvg) (Opt.)
xvgr/xmgr file
-life [<.xvg>] (hblife.xvg) (Opt.)
xvgr/xmgr file
-nhbdist [<.xvg>] (nhbdist.xvg) (Opt.)
xvgr/xmgr file
Other options:
-b <time> (0)
Time of first frame to read from trajectory (default unit ps)
-e <time> (0)
Time of last frame to read from trajectory (default unit ps)
-dt <time> (0)
Only use frame when t MOD dt = first time (default unit ps)
-tu <enum> (ps)
Unit for time values: fs, ps, ns, us, ms, s
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-a <real> (30)
Cutoff angle (degrees, Hydrogen - Donor - 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)
-r2 <real> (0)
Second cutoff radius. Mainly useful with -contact and -ac
-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 (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
-fitend <real> (60)
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)
-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
hydrogen are treated as a single H-bond. Mainly important for the
ACF. Not compatible with options that depend on knowing a specific
hydrogen: -noad, -ang.
-nthreads <int> (0)
Number of threads used for the parallel loop over autocorrelations.
nThreads <= 0 means maximum number of threads. Requires linking
with OpenMP. The number of threads is limited by the number of
cores (before OpenMP v.3 ) or environment variable OMP_THREAD_LIMIT
(OpenMP v.3)
-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, 3
-fitfn <enum> (none)
Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
-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 until the end
GROMACS reminds you: "That Was Pretty Cool" (Beavis)
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发表于 Post on 2024-6-21 12:08:14
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楼主 Author
发表于 Post on 2024-6-22 02:41:24