| VERSION 4.5 |
g_cluster can cluster structures with several different methods. Distances between structures can be determined from a trajectory or read from an XPM matrix file with the -dm option. RMS deviation after fitting or RMS deviation of atom-pair distances can be used to define the distance between structures.
single linkage: add a structure to a cluster when its distance to any element of the cluster is less than cutoff.
Jarvis Patrick: add a structure to a cluster when this structure and a structure in the cluster have each other as neighbors and they have a least P neighbors in common. The neighbors of a structure are the M closest structures or all structures within cutoff.
Monte Carlo: reorder the RMSD matrix using Monte Carlo.
diagonalization: diagonalize the RMSD matrix.
gromos: use algorithm as described in Daura
When the clustering algorithm assigns each structure to exactly one cluster (single linkage, Jarvis Patrick and gromos) and a trajectory file is supplied, the structure with the smallest average distance to the others or the average structure or all structures for each cluster will be written to a trajectory file. When writing all structures, separate numbered files are made for each cluster.
Two output files are always written:
-o writes the RMSD values in the upper left half of the matrix
and a graphical depiction of the clusters in the lower right half
When -minstruct = 1 the graphical depiction is black
when two structures are in the same cluster.
When -minstruct > 1 different colors will be used for each
cluster.
-g writes information on the options used and a detailed list
of all clusters and their members.
Additionally, a number of optional output files can be written:
-dist writes the RMSD distribution.
-ev writes the eigenvectors of the RMSD matrix
diagonalization.
-sz writes the cluster sizes.
-tr writes a matrix of the number transitions between
cluster pairs.
-ntr writes the total number of transitions to or from
each cluster.
-clid writes the cluster number as a function of time.
-cl writes average (with option -av) or central
structure of each cluster or writes numbered files with cluster members
for a selected set of clusters (with option -wcl, depends on
-nst and -rmsmin).
option | filename | type | description |
---|---|---|---|
-f | traj.xtc | Input, Opt. | Trajectory: xtc trr trj gro g96 pdb cpt |
-s | topol.tpr | Input, Opt. | Structure+mass(db): tpr tpb tpa gro g96 pdb |
-n | index.ndx | Input, Opt. | Index file |
-dm | rmsd.xpm | Input, Opt. | X PixMap compatible matrix file |
-o | rmsd-clust.xpm | Output | X PixMap compatible matrix file |
-g | cluster.log | Output | Log file |
-dist | rmsd-dist.xvg | Output, Opt. | xvgr/xmgr file |
-ev | rmsd-eig.xvg | Output, Opt. | xvgr/xmgr file |
-sz | clust-size.xvg | Output, Opt. | xvgr/xmgr file |
-tr | clust-trans.xpm | Output, Opt. | X PixMap compatible matrix file |
-ntr | clust-trans.xvg | Output, Opt. | xvgr/xmgr file |
-clid | clust-id.xvg | Output, Opt. | xvgr/xmgr file |
-cl | clusters.pdb | Output, Opt. | Trajectory: xtc trr trj gro g96 pdb cpt |
option | type | default | description |
---|---|---|---|
-[no]h | gmx_bool | no | Print help info and quit |
-[no]version | gmx_bool | no | Print version info and quit |
-nice | int | 19 | Set the nicelevel |
-b | time | 0 | First frame (ps) to read from trajectory |
-e | time | 0 | Last frame (ps) to read from trajectory |
-dt | time | 0 | Only use frame when t MOD dt = first time (ps) |
-tu | enum | ps | Time unit: fs, ps, ns, us, ms or s |
-[no]w | gmx_bool | no | View output xvg, xpm, eps and pdb files |
-xvg | enum | xmgrace | xvg plot formatting: xmgrace, xmgr or none |
-[no]dista | gmx_bool | no | Use RMSD of distances instead of RMS deviation |
-nlevels | int | 40 | Discretize RMSD matrix in # levels |
-cutoff | real | 0.1 | RMSD cut-off (nm) for two structures to be neighbor |
-[no]fit | gmx_bool | yes | Use least squares fitting before RMSD calculation |
-max | real | -1 | Maximum level in RMSD matrix |
-skip | int | 1 | Only analyze every nr-th frame |
-[no]av | gmx_bool | no | Write average iso middle structure for each cluster |
-wcl | int | 0 | Write all structures for first # clusters to numbered files |
-nst | int | 1 | Only write all structures if more than # per cluster |
-rmsmin | real | 0 | minimum rms difference with rest of cluster for writing structures |
-method | enum | linkage | Method for cluster determination: linkage, jarvis-patrick, monte-carlo, diagonalization or gromos |
-minstruct | int | 1 | Minimum number of structures in cluster for coloring in the xpm file |
-[no]binary | gmx_bool | no | Treat the RMSD matrix as consisting of 0 and 1, where the cut-off is given by -cutoff |
-M | int | 10 | Number of nearest neighbors considered for Jarvis-Patrick algorithm, 0 is use cutoff |
-P | int | 3 | Number of identical nearest neighbors required to form a cluster |
-seed | int | 1993 | Random number seed for Monte Carlo clustering algorithm |
-niter | int | 10000 | Number of iterations for MC |
-kT | real | 0.001 | Boltzmann weighting factor for Monte Carlo optimization (zero turns off uphill steps) |