1GMX-DENSORDER(1)                    GROMACS                   GMX-DENSORDER(1)
2
3
4

NAME

6       gmx-densorder - Calculate surface fluctuations
7

SYNOPSIS

9          gmx densorder [-s [<.tpr>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
10                       [-o [<.dat>]] [-or [<.out> [...]]] [-og [<.xpm> [...]]]
11                       [-Spect [<.out> [...]]] [-b <time>] [-e <time>]
12                       [-dt <time>] [-[no]w] [-[no]1d] [-bw <real>]
13                       [-bwn <real>] [-order <int>] [-axis <string>]
14                       [-method <enum>] [-d1 <real>] [-d2 <real>]
15                       [-tblock <int>] [-nlevel <int>]
16

DESCRIPTION

18       gmx  densorder  reduces a two-phase density distribution along an axis,
19       computed over a MD trajectory, to 2D surfaces fluctuating in time, by a
20       fit to a functional profile for interfacial densities.  A time-averaged
21       spatial representation of the interfaces can be output with the  option
22       -tavg.
23

OPTIONS

25       Options to specify input files:
26
27       -s [<.tpr>] (topol.tpr)
28              Portable xdr run input file
29
30       -f [<.xtc/.trr/…>] (traj.xtc)
31              Trajectory: xtc trr cpt gro g96 pdb tng
32
33       -n [<.ndx>] (index.ndx)
34              Index file
35
36       Options to specify output files:
37
38       -o [<.dat>] (Density4D.dat) (Optional)
39              Generic data file
40
41       -or [<.out> […]] (hello.out) (Optional)
42              Generic output file
43
44       -og [<.xpm> […]] (interface.xpm) (Optional)
45              X PixMap compatible matrix file
46
47       -Spect [<.out> […]] (intfspect.out) (Optional)
48              Generic output file
49
50       Other options:
51
52       -b <time> (0)
53              Time of first frame to read from trajectory (default unit ps)
54
55       -e <time> (0)
56              Time of last frame to read from trajectory (default unit ps)
57
58       -dt <time> (0)
59              Only use frame when t MOD dt = first time (default unit ps)
60
61       -[no]w (no)
62              View output .xvg, .xpm, .eps and .pdb files
63
64       -[no]1d (no)
65              Pseudo-1d interface geometry
66
67       -bw <real> (0.2)
68              Binwidth of density distribution tangential to interface
69
70       -bwn <real> (0.05)
71              Binwidth of density distribution normal to interface
72
73       -order <int> (0)
74              Order of Gaussian filter, order 0 equates to NO filtering
75
76       -axis <string> (Z)
77              Axis Direction - X, Y or Z
78
79       -method <enum> (bisect)
80              Interface location method: bisect, functional
81
82       -d1 <real> (0)
83              Bulk density phase 1 (at small z)
84
85       -d2 <real> (1000)
86              Bulk density phase 2 (at large z)
87
88       -tblock <int> (100)
89              Number of frames in one time-block average
90
91       -nlevel <int> (100)
92              Number of Height levels in 2D - XPixMaps
93

SEE ALSO

95       gmx(1)
96
97       More     information    about    GROMACS    is    available    at    <‐
98       http://www.gromacs.org/>.
99

101       2019, GROMACS development team
102
103
104
105
1062018.7                           May 29, 2019                 GMX-DENSORDER(1)
Impressum