1 .TH g_clustsize 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
3 g_clustsize - calculate size distributions of atomic clusters
9 .BI "\-s" " topol.tpr "
10 .BI "\-n" " index.ndx "
11 .BI "\-o" " csize.xpm "
12 .BI "\-ow" " csizew.xpm "
13 .BI "\-nc" " nclust.xvg "
14 .BI "\-mc" " maxclust.xvg "
15 .BI "\-ac" " avclust.xvg "
16 .BI "\-hc" " histo\-clust.xvg "
17 .BI "\-temp" " temp.xvg "
18 .BI "\-mcn" " maxclust.ndx "
20 .BI "\-[no]version" ""
32 .BI "\-nlevels" " int "
34 .BI "\-rgblo" " vector "
35 .BI "\-rgbhi" " vector "
37 \&This program computes the size distributions of molecular/atomic clusters in
38 \&the gas phase. The output is given in the form of a XPM file.
39 \&The total number of clusters is written to a XVG file.
42 \&When the \fB \-mol\fR option is given clusters will be made out of
43 \&molecules rather than atoms, which allows clustering of large molecules.
44 \&In this case an index file would still contain atom numbers
45 \&or your calculation will die with a SEGV.
48 \&When velocities are present in your trajectory, the temperature of
49 \&the largest cluster will be printed in a separate xvg file assuming
50 \&that the particles are free to move. If you are using constraints,
51 \&please correct the temperature. For instance water simulated with SHAKE
52 \&or SETTLE will yield a temperature that is 1.5 times too low. You can
53 \&compensate for this with the \-ndf option. Remember to take the removal
54 \&of center of mass motion into account.
57 \&The \fB \-mc\fR option will produce an index file containing the
58 \&atom numbers of the largest cluster.
62 Trajectory: xtc trr trj gro g96 pdb cpt
64 .BI "\-s" " topol.tpr"
66 Portable xdr run input file
68 .BI "\-n" " index.ndx"
72 .BI "\-o" " csize.xpm"
74 X PixMap compatible matrix file
76 .BI "\-ow" " csizew.xpm"
78 X PixMap compatible matrix file
80 .BI "\-nc" " nclust.xvg"
84 .BI "\-mc" " maxclust.xvg"
88 .BI "\-ac" " avclust.xvg"
92 .BI "\-hc" " histo\-clust.xvg"
96 .BI "\-temp" " temp.xvg"
100 .BI "\-mcn" " maxclust.ndx"
106 Print help info and quit
108 .BI "\-[no]version" "no "
109 Print version info and quit
111 .BI "\-nice" " int" " 19"
114 .BI "\-b" " time" " 0 "
115 First frame (ps) to read from trajectory
117 .BI "\-e" " time" " 0 "
118 Last frame (ps) to read from trajectory
120 .BI "\-dt" " time" " 0 "
121 Only use frame when t MOD dt = first time (ps)
123 .BI "\-tu" " enum" " ps"
124 Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR
127 View output xvg, xpm, eps and pdb files
129 .BI "\-xvg" " enum" " xmgrace"
130 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
132 .BI "\-cut" " real" " 0.35 "
133 Largest distance (nm) to be considered in a cluster
135 .BI "\-[no]mol" "no "
136 Cluster molecules rather than atoms (needs tpr file)
138 .BI "\-[no]pbc" "yes "
139 Use periodic boundary conditions
141 .BI "\-nskip" " int" " 0"
142 Number of frames to skip between writing
144 .BI "\-nlevels" " int" " 20"
145 Number of levels of grey in xpm output
147 .BI "\-ndf" " int" " \-1"
148 Number of degrees of freedom of the entire system for temperature calculation. If not set, the number of atoms times three is used.
150 .BI "\-rgblo" " vector" " 1 1 0"
151 RGB values for the color of the lowest occupied cluster size
153 .BI "\-rgbhi" " vector" " 0 0 1"
154 RGB values for the color of the highest occupied cluster size
159 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.