1g_cluster(1) GROMACS suite, VERSION 4.5 g_cluster(1)
2
6 g_cluster - clusters structures
7 VERSION 4.5
9
11 g_cluster -f traj.xtc -s topol.tpr -n index.ndx -dm rmsd.xpm -o
12 rmsd-clust.xpm -g cluster.log -dist rmsd-dist.xvg -ev rmsd-eig.xvg -sz
13 clust-size.xvg -tr clust-trans.xpm -ntr clust-trans.xvg -clid
14 clust-id.xvg -cl clusters.pdb -[no]h -[no]version -nice int -b time -e
15 time -dt time -tu enum -[no]w -xvg enum -[no]dista -nlevels int -cutoff
16 real -[no]fit -max real -skip int -[no]av -wcl int -nst int -rmsmin
17 real -method enum -minstruct int -[no]binary -M int -P int -seed int
18 -niter int -kT real
19
21 g_cluster can cluster structures with several different methods. Dis‐
22 tances between structures can be determined from a trajectory or read
23 from an XPM matrix file with the -dm option. RMS deviation after fit‐
24 ting or RMS deviation of atom-pair distances can be used to define the
25 distance between structures.
26 single linkage: add a structure to a cluster when its distance to any
29 element of the cluster is less than cutoff.
30 Jarvis Patrick: add a structure to a cluster when this structure and a
33 structure in the cluster have each other as neighbors and they have a
34 least P neighbors in common. The neighbors of a structure are the M
35 closest structures or all structures within cutoff.
36 Monte Carlo: reorder the RMSD matrix using Monte Carlo.
39 diagonalization: diagonalize the RMSD matrix.
42 gromos: use algorithm as described in Daura et al. ( Angew. Chem.
45 Int. Ed. 1999, 38, pp 236-240). Count number of neighbors using
46 cut-off, take structure with largest number of neighbors with all its
47 neighbors as cluster and eleminate it from the pool of clusters. Repeat
48 for remaining structures in pool.
49 When the clustering algorithm assigns each structure to exactly one
52 cluster (single linkage, Jarvis Patrick and gromos) and a trajectory
53 file is supplied, the structure with the smallest average distance to
54 the others or the average structure or all structures for each cluster
55 will be written to a trajectory file. When writing all structures, sep‐
56 arate numbered files are made for each cluster.
57 Two output files are always written:
60 -o writes the RMSD values in the upper left half of the matrix and a
62 graphical depiction of the clusters in the lower right half When -min‐
63 struct = 1 the graphical depiction is black when two structures are in
64 the same cluster. When -minstruct 1 different colors will be used
65 for each cluster.
66 -g writes information on the options used and a detailed list of all
68 clusters and their members.
69 Additionally, a number of optional output files can be written:
72 -dist writes the RMSD distribution.
74 -ev writes the eigenvectors of the RMSD matrix diagonalization.
76 -sz writes the cluster sizes.
78 -tr writes a matrix of the number transitions between cluster pairs.
80 -ntr writes the total number of transitions to or from each cluster.
82 -clid writes the cluster number as a function of time.
84 -cl writes average (with option -av) or central structure of each
86 cluster or writes numbered files with cluster members for a selected
87 set of clusters (with option -wcl, depends on -nst and -rmsmin).
88
91 -f traj.xtc Input, Opt.
92 Trajectory: xtc trr trj gro g96 pdb cpt
93 -s topol.tpr Input, Opt.
95 Structure+mass(db): tpr tpb tpa gro g96 pdb
96 -n index.ndx Input, Opt.
98 Index file
99 -dm rmsd.xpm Input, Opt.
101 X PixMap compatible matrix file
102 -o rmsd-clust.xpm Output
104 X PixMap compatible matrix file
105 -g cluster.log Output
107 Log file
108 -dist rmsd-dist.xvg Output, Opt.
110 xvgr/xmgr file
111 -ev rmsd-eig.xvg Output, Opt.
113 xvgr/xmgr file
114 -sz clust-size.xvg Output, Opt.
116 xvgr/xmgr file
117 -tr clust-trans.xpm Output, Opt.
119 X PixMap compatible matrix file
120 -ntr clust-trans.xvg Output, Opt.
122 xvgr/xmgr file
123 -clid clust-id.xvg Output, Opt.
125 xvgr/xmgr file
126 -cl clusters.pdb Output, Opt.
128 Trajectory: xtc trr trj gro g96 pdb cpt
129
132 -[no]hno
133 Print help info and quit
134 -[no]versionno
136 Print version info and quit
137 -nice int 19
139 Set the nicelevel
140 -b time 0
142 First frame (ps) to read from trajectory
143 -e time 0
145 Last frame (ps) to read from trajectory
146 -dt time 0
148 Only use frame when t MOD dt = first time (ps)
149 -tu enum ps
151 Time unit: fs, ps, ns, us, ms or s
152 -[no]wno
154 View output xvg, xpm, eps and pdb files
155 -xvg enum xmgrace
157 xvg plot formatting: xmgrace, xmgr or none
158 -[no]distano
160 Use RMSD of distances instead of RMS deviation
161 -nlevels int 40
163 Discretize RMSD matrix in levels
164 -cutoff real 0.1
166 RMSD cut-off (nm) for two structures to be neighbor
167 -[no]fityes
169 Use least squares fitting before RMSD calculation
170 -max real -1
172 Maximum level in RMSD matrix
173 -skip int 1
175 Only analyze every nr-th frame
176 -[no]avno
178 Write average iso middle structure for each cluster
179 -wcl int 0
181 Write all structures for first clusters to numbered files
182 -nst int 1
184 Only write all structures if more than per cluster
185 -rmsmin real 0
187 minimum rms difference with rest of cluster for writing structures
188 -method enum linkage
190 Method for cluster determination: linkage, jarvis-patrick,
191 monte-carlo, diagonalization or gromos
192 -minstruct int 1
194 Minimum number of structures in cluster for coloring in the xpm file
195 -[no]binaryno
197 Treat the RMSD matrix as consisting of 0 and 1, where the cut-off is
198 given by -cutoff
199 -M int 10
201 Number of nearest neighbors considered for Jarvis-Patrick algorithm, 0
202 is use cutoff
203 -P int 3
205 Number of identical nearest neighbors required to form a cluster
206 -seed int 1993
208 Random number seed for Monte Carlo clustering algorithm
209 -niter int 10000
211 Number of iterations for MC
212 -kT real 0.001
214 Boltzmann weighting factor for Monte Carlo optimization (zero turns
215 off uphill steps)
216
219 gromacs(7)
220 More information about GROMACS is available at <http://www.gro‐
222 macs.org/>.
223 Thu 26 Aug 2010 g_cluster(1)