1GMX-CLUSTSIZE(1)                    GROMACS                   GMX-CLUSTSIZE(1)
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NAME

6       gmx-clustsize - Calculate size distributions of atomic clusters
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SYNOPSIS

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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DESCRIPTION

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.
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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.
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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.
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36       The -mc option will produce an index file containing the  atom  numbers
37       of the largest cluster.
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OPTIONS

40       Options to specify input files:
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42       -f [<.xtc/.trr/…>] (traj.xtc)
43              Trajectory: xtc trr cpt gro g96 pdb tng
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45       -s [<.tpr>] (topol.tpr) (Optional)
46              Portable xdr run input file
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48       -n [<.ndx>] (index.ndx) (Optional)
49              Index file
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51       Options to specify output files:
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53       -o [<.xpm>] (csize.xpm)
54              X PixMap compatible matrix file
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56       -ow [<.xpm>] (csizew.xpm)
57              X PixMap compatible matrix file
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59       -nc [<.xvg>] (nclust.xvg)
60              xvgr/xmgr file
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62       -mc [<.xvg>] (maxclust.xvg)
63              xvgr/xmgr file
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65       -ac [<.xvg>] (avclust.xvg)
66              xvgr/xmgr file
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68       -hc [<.xvg>] (histo-clust.xvg)
69              xvgr/xmgr file
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71       -temp [<.xvg>] (temp.xvg) (Optional)
72              xvgr/xmgr file
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74       -mcn [<.ndx>] (maxclust.ndx) (Optional)
75              Index file
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77       Other options:
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79       -b <time> (0)
80              Time of first frame to read from trajectory (default unit ps)
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82       -e <time> (0)
83              Time of last frame to read from trajectory (default unit ps)
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85       -dt <time> (0)
86              Only use frame when t MOD dt = first time (default unit ps)
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88       -tu <enum> (ps)
89              Unit for time values: fs, ps, ns, us, ms, s
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91       -[no]w (no)
92              View output .xvg, .xpm, .eps and .pdb files
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94       -xvg <enum> (xmgrace)
95              xvg plot formatting: xmgrace, xmgr, none
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97       -cut <real> (0.35)
98              Largest distance (nm) to be considered in a cluster
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100       -[no]mol (no)
101              Cluster molecules rather than atoms (needs .tpr file)
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103       -[no]pbc (yes)
104              Use periodic boundary conditions
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106       -nskip <int> (0)
107              Number of frames to skip between writing
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109       -nlevels <int> (20)
110              Number of levels of grey in .xpm output
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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.
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117       -rgblo <vector> (1 1 0)
118              RGB values for the color of the lowest occupied cluster size
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120       -rgbhi <vector> (0 0 1)
121              RGB values for the color of the highest occupied cluster size
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SEE ALSO

124       gmx(1)
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126       More     information    about    GROMACS    is    available    at    <‐
127       http://www.gromacs.org/>.
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130       2020, GROMACS development team
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1352019.6                           Feb 28, 2020                 GMX-CLUSTSIZE(1)
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