1GMX-CLUSTSIZE(1) GROMACS GMX-CLUSTSIZE(1)
2
3
4
6 gmx-clustsize - Calculate size distributions of atomic clusters
7
9 gmx clustsize [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-n [<.ndx>]]
10 [-o [<.xpm>]] [-ow [<.xpm>]] [-nc [<.xvg>]]
11 [-mc [<.xvg>]] [-ac [<.xvg>]] [-hc [<.xvg>]]
12 [-temp [<.xvg>]] [-mcn [<.ndx>]] [-b <time>] [-e <time>]
13 [-dt <time>] [-tu <enum>] [-[no]w] [-xvg <enum>]
14 [-cut <real>] [-[no]mol] [-[no]pbc] [-nskip <int>]
15 [-nlevels <int>] [-ndf <int>] [-rgblo <vector>]
16 [-rgbhi <vector>]
17
19 gmx clustsize computes the size distributions of molecular/atomic clus‐
20 ters in the gas phase. The output is given in the form of an .xpm file.
21 The total number of clusters is written to an .xvg file.
22
23 When the -mol option is given clusters will be made out of molecules
24 rather than atoms, which allows clustering of large molecules. In this
25 case an index file would still contain atom numbers or your calculation
26 will die with a SEGV.
27
28 When velocities are present in your trajectory, the temperature of the
29 largest cluster will be printed in a separate .xvg file assuming that
30 the particles are free to move. If you are using constraints, please
31 correct the temperature. For instance water simulated with SHAKE or
32 SETTLE will yield a temperature that is 1.5 times too low. You can com‐
33 pensate for this with the -ndf option. Remember to take the removal of
34 center of mass motion into account.
35
36 The -mc option will produce an index file containing the atom numbers
37 of the largest cluster.
38
40 Options to specify input files:
41
42 -f [<.xtc/.trr/…>] (traj.xtc)
43 Trajectory: xtc trr cpt gro g96 pdb tng
44
45 -s [<.tpr>] (topol.tpr) (Optional)
46 Portable xdr run input file
47
48 -n [<.ndx>] (index.ndx) (Optional)
49 Index file
50
51 Options to specify output files:
52
53 -o [<.xpm>] (csize.xpm)
54 X PixMap compatible matrix file
55
56 -ow [<.xpm>] (csizew.xpm)
57 X PixMap compatible matrix file
58
59 -nc [<.xvg>] (nclust.xvg)
60 xvgr/xmgr file
61
62 -mc [<.xvg>] (maxclust.xvg)
63 xvgr/xmgr file
64
65 -ac [<.xvg>] (avclust.xvg)
66 xvgr/xmgr file
67
68 -hc [<.xvg>] (histo-clust.xvg)
69 xvgr/xmgr file
70
71 -temp [<.xvg>] (temp.xvg) (Optional)
72 xvgr/xmgr file
73
74 -mcn [<.ndx>] (maxclust.ndx) (Optional)
75 Index file
76
77 Other options:
78
79 -b <time> (0)
80 Time of first frame to read from trajectory (default unit ps)
81
82 -e <time> (0)
83 Time of last frame to read from trajectory (default unit ps)
84
85 -dt <time> (0)
86 Only use frame when t MOD dt = first time (default unit ps)
87
88 -tu <enum> (ps)
89 Unit for time values: fs, ps, ns, us, ms, s
90
91 -[no]w (no)
92 View output .xvg, .xpm, .eps and .pdb files
93
94 -xvg <enum> (xmgrace)
95 xvg plot formatting: xmgrace, xmgr, none
96
97 -cut <real> (0.35)
98 Largest distance (nm) to be considered in a cluster
99
100 -[no]mol (no)
101 Cluster molecules rather than atoms (needs .tpr file)
102
103 -[no]pbc (yes)
104 Use periodic boundary conditions
105
106 -nskip <int> (0)
107 Number of frames to skip between writing
108
109 -nlevels <int> (20)
110 Number of levels of grey in .xpm output
111
112 -ndf <int> (-1)
113 Number of degrees of freedom of the entire system for tempera‐
114 ture calculation. If not set, the number of atoms times three is
115 used.
116
117 -rgblo <vector> (1 1 0)
118 RGB values for the color of the lowest occupied cluster size
119
120 -rgbhi <vector> (0 0 1)
121 RGB values for the color of the highest occupied cluster size
122
124 gmx(1)
125
126 More information about GROMACS is available at <‐
127 http://www.gromacs.org/>.
128
130 2019, GROMACS development team
131
132
133
134
1352019.2 Apr 16, 2019 GMX-CLUSTSIZE(1)