g_clustsize(1)

1g_clustsize(1)            GROMACS suite, VERSION 4.5            g_clustsize(1)
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NAME

6       g_clustsize - calculate size distributions of atomic clusters
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8       VERSION 4.5
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SYNOPSIS

11       g_clustsize  -f  traj.xtc  -s  topol.tpr  -n index.ndx -o csize.xpm -ow
12       csizew.xpm  -nc  nclust.xvg  -mc  maxclust.xvg  -ac   avclust.xvg   -hc
13       histo-clust.xvg  -temp  temp.xvg  -mcn maxclust.ndx -[no]h -[no]version
14       -nice int -b time -e time -dt time -tu enum -[no]w -xvg enum -cut  real
15       -[no]mol -[no]pbc -nskip int -nlevels int -ndf int -rgblo vector -rgbhi
16       vector
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DESCRIPTION

19       This program computes the size distributions of molecular/atomic  clus‐
20       ters  in  the gas phase. The output is given in the form of a XPM file.
21       The total number of clusters is written to a XVG file.
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24       When the  -mol option is given clusters will be made out  of  molecules
25       rather than atoms, which allows clustering of large molecules.  In this
26       case an index file would still contain atom numbers or your calculation
27       will die with a SEGV.
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30       When  velocities are present in your trajectory, the temperature of the
31       largest cluster will be printed in a separate xvg  file  assuming  that
32       the  particles  are  free to move. If you are using constraints, please
33       correct the temperature. For instance water  simulated  with  SHAKE  or
34       SETTLE will yield a temperature that is 1.5 times too low. You can com‐
35       pensate for this with the -ndf option. Remember to take the removal  of
36       center of mass motion into account.
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39       The   -mc option will produce an index file containing the atom numbers
40       of the largest cluster.
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FILES

43       -f traj.xtc Input
44        Trajectory: xtc trr trj gro g96 pdb cpt
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46       -s topol.tpr Input, Opt.
47        Portable xdr run input file
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49       -n index.ndx Input, Opt.
50        Index file
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52       -o csize.xpm Output
53        X PixMap compatible matrix file
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55       -ow csizew.xpm Output
56        X PixMap compatible matrix file
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58       -nc nclust.xvg Output
59        xvgr/xmgr file
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61       -mc maxclust.xvg Output
62        xvgr/xmgr file
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64       -ac avclust.xvg Output
65        xvgr/xmgr file
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67       -hc histo-clust.xvg Output
68        xvgr/xmgr file
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70       -temp temp.xvg Output, Opt.
71        xvgr/xmgr file
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73       -mcn maxclust.ndx Output, Opt.
74        Index file
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OTHER OPTIONS

78       -[no]hno
79        Print help info and quit
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81       -[no]versionno
82        Print version info and quit
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84       -nice int 19
85        Set the nicelevel
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87       -b time 0
88        First frame (ps) to read from trajectory
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90       -e time 0
91        Last frame (ps) to read from trajectory
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93       -dt time 0
94        Only use frame when t MOD dt = first time (ps)
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96       -tu enum ps
97        Time unit:  fs,  ps,  ns,  us,  ms or  s
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99       -[no]wno
100        View output xvg, xpm, eps and pdb files
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102       -xvg enum xmgrace
103        xvg plot formatting:  xmgrace,  xmgr or  none
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105       -cut real 0.35
106        Largest distance (nm) to be considered in a cluster
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108       -[no]molno
109        Cluster molecules rather than atoms (needs tpr file)
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111       -[no]pbcyes
112        Use periodic boundary conditions
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114       -nskip int 0
115        Number of frames to skip between writing
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117       -nlevels int 20
118        Number of levels of grey in xpm output
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120       -ndf int -1
121        Number of degrees of freedom of the entire system for temperature cal‐
122       culation. If not set, the number of atoms times three is used.
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124       -rgblo vector 1 1 0
125        RGB values for the color of the lowest occupied cluster size
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127       -rgbhi vector 0 0 1
128        RGB values for the color of the highest occupied cluster size
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NAME

SYNOPSIS

DESCRIPTION

FILES

OTHER OPTIONS

SEE ALSO