1GMX-CLUSTSIZE(1) GROMACS GMX-CLUSTSIZE(1)
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6 gmx-clustsize - Calculate size distributions of atomic clusters
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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>]
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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 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 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 The -mc option will produce an index file containing the atom numbers
37 of the largest cluster.
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40 Options to specify input files:
41 -f [<.xtc/.trr/…>] (traj.xtc)
43 Trajectory: xtc trr cpt gro g96 pdb tng
44 -s [<.tpr>] (topol.tpr) (Optional)
46 Portable xdr run input file
47 -n [<.ndx>] (index.ndx) (Optional)
49 Index file
50 Options to specify output files:
52 -o [<.xpm>] (csize.xpm)
54 X PixMap compatible matrix file
55 -ow [<.xpm>] (csizew.xpm)
57 X PixMap compatible matrix file
58 -nc [<.xvg>] (nclust.xvg)
60 xvgr/xmgr file
61 -mc [<.xvg>] (maxclust.xvg)
63 xvgr/xmgr file
64 -ac [<.xvg>] (avclust.xvg)
66 xvgr/xmgr file
67 -hc [<.xvg>] (histo-clust.xvg)
69 xvgr/xmgr file
70 -temp [<.xvg>] (temp.xvg) (Optional)
72 xvgr/xmgr file
73 -mcn [<.ndx>] (maxclust.ndx) (Optional)
75 Index file
76 Other options:
78 -b <time> (0)
80 Time of first frame to read from trajectory (default unit ps)
81 -e <time> (0)
83 Time of last frame to read from trajectory (default unit ps)
84 -dt <time> (0)
86 Only use frame when t MOD dt = first time (default unit ps)
87 -tu <enum> (ps)
89 Unit for time values: fs, ps, ns, us, ms, s
90 -[no]w (no)
92 View output .xvg, .xpm, .eps and .pdb files
93 -xvg <enum> (xmgrace)
95 xvg plot formatting: xmgrace, xmgr, none
96 -cut <real> (0.35)
98 Largest distance (nm) to be considered in a cluster
99 -[no]mol (no)
101 Cluster molecules rather than atoms (needs .tpr file)
102 -[no]pbc (yes)
104 Use periodic boundary conditions
105 -nskip <int> (0)
107 Number of frames to skip between writing
108 -nlevels <int> (20)
110 Number of levels of grey in .xpm output
111 -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 -rgblo <vector> (1 1 0)
118 RGB values for the color of the lowest occupied cluster size
119 -rgbhi <vector> (0 0 1)
121 RGB values for the color of the highest occupied cluster size
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124 gmx(1)
125 More information about GROMACS is available at <‐
127 http://www.gromacs.org/>.
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130 2020, GROMACS development team
1312019.6 Feb 28, 2020 GMX-CLUSTSIZE(1)