1GMX-CLUSTER(1) GROMACS GMX-CLUSTER(1)
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6 gmx-cluster - Cluster structures
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9 gmx cluster [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10 [-dm [<.xpm>]] [-om [<.xpm>]] [-o [<.xpm>]] [-g [<.log>]]
11 [-dist [<.xvg>]] [-ev [<.xvg>]] [-conv [<.xvg>]]
12 [-sz [<.xvg>]] [-tr [<.xpm>]] [-ntr [<.xvg>]]
13 [-clid [<.xvg>]] [-cl [<.xtc/.trr/...>]] [-b <time>]
14 [-e <time>] [-dt <time>] [-tu <enum>] [-[no]w]
15 [-xvg <enum>] [-[no]dista] [-nlevels <int>]
16 [-cutoff <real>] [-[no]fit] [-max <real>] [-skip <int>]
17 [-[no]av] [-wcl <int>] [-nst <int>] [-rmsmin <real>]
18 [-method <enum>] [-minstruct <int>] [-[no]binary]
19 [-M <int>] [-P <int>] [-seed <int>] [-niter <int>]
20 [-nrandom <int>] [-kT <real>] [-[no]pbc]
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23 gmx cluster can cluster structures using several different methods.
24 Distances between structures can be determined from a trajectory or
25 read from an .xpm matrix file with the -dm option. RMS deviation after
26 fitting or RMS deviation of atom-pair distances can be used to define
27 the distance between structures.
28 single linkage: add a structure to a cluster when its distance to any
30 element of the cluster is less than cutoff.
31 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 such that the
38 order of the frames is using the smallest possible increments. With
39 this it is possible to make a smooth animation going from one structure
40 to another with the largest possible (e.g.) RMSD between them, however
41 the intermediate steps should be as small as possible. Applications
42 could be to visualize a potential of mean force ensemble of simulations
43 or a pulling simulation. Obviously the user has to prepare the trajec‐
44 tory well (e.g. by not superimposing frames). The final result can be
45 inspect visually by looking at the matrix .xpm file, which should vary
46 smoothly from bottom to top.
47 diagonalization: diagonalize the RMSD matrix.
49 gromos: use algorithm as described in Daura et al. (Angew. Chem. Int.
51 Ed. 1999, 38, pp 236-240). Count number of neighbors using cut-off,
52 take structure with largest number of neighbors with all its neighbors
53 as cluster and eliminate it from the pool of clusters. Repeat for
54 remaining structures in pool.
55 When the clustering algorithm assigns each structure to exactly one
57 cluster (single linkage, Jarvis Patrick and gromos) and a trajectory
58 file is supplied, the structure with the smallest average distance to
59 the others or the average structure or all structures for each cluster
60 will be written to a trajectory file. When writing all structures, sep‐
61 arate numbered files are made for each cluster.
62 Two output files are always written:
64 · -o writes the RMSD values in the upper left half of the matrix and
66 a graphical depiction of the clusters in the lower right half When
67 -minstruct = 1 the graphical depiction is black when two struc‐
68 tures are in the same cluster. When -minstruct > 1 different col‐
69 ors will be used for each cluster.
70 · -g writes information on the options used and a detailed list of
72 all clusters and their members.
73 Additionally, a number of optional output files can be written:
75 · -dist writes the RMSD distribution.
77 · -ev writes the eigenvectors of the RMSD matrix diagonalization.
79 · -sz writes the cluster sizes.
81 · -tr writes a matrix of the number transitions between cluster
83 pairs.
84 · -ntr writes the total number of transitions to or from each clus‐
86 ter.
87 · -clid writes the cluster number as a function of time.
89 · -cl writes average (with option -av) or central structure of each
91 cluster or writes numbered files with cluster members for a
92 selected set of clusters (with option -wcl, depends on -nst and
93 -rmsmin). The center of a cluster is the structure with the small‐
94 est average RMSD from all other structures of the cluster.
95
97 Options to specify input files:
98 -f [<.xtc/.trr/…>] (traj.xtc) (Optional)
100 Trajectory: xtc trr cpt gro g96 pdb tng
101 -s [<.tpr/.gro/…>] (topol.tpr)
103 Structure+mass(db): tpr gro g96 pdb brk ent
104 -n [<.ndx>] (index.ndx) (Optional)
106 Index file
107 -dm [<.xpm>] (rmsd.xpm) (Optional)
109 X PixMap compatible matrix file
110 Options to specify output files:
112 -om [<.xpm>] (rmsd-raw.xpm)
114 X PixMap compatible matrix file
115 -o [<.xpm>] (rmsd-clust.xpm)
117 X PixMap compatible matrix file
118 -g [<.log>] (cluster.log)
120 Log file
121 -dist [<.xvg>] (rmsd-dist.xvg) (Optional)
123 xvgr/xmgr file
124 -ev [<.xvg>] (rmsd-eig.xvg) (Optional)
126 xvgr/xmgr file
127 -conv [<.xvg>] (mc-conv.xvg) (Optional)
129 xvgr/xmgr file
130 -sz [<.xvg>] (clust-size.xvg) (Optional)
132 xvgr/xmgr file
133 -tr [<.xpm>] (clust-trans.xpm) (Optional)
135 X PixMap compatible matrix file
136 -ntr [<.xvg>] (clust-trans.xvg) (Optional)
138 xvgr/xmgr file
139 -clid [<.xvg>] (clust-id.xvg) (Optional)
141 xvgr/xmgr file
142 -cl [<.xtc/.trr/…>] (clusters.pdb) (Optional)
144 Trajectory: xtc trr cpt gro g96 pdb tng
145 Other options:
147 -b <time> (0)
149 Time of first frame to read from trajectory (default unit ps)
150 -e <time> (0)
152 Time of last frame to read from trajectory (default unit ps)
153 -dt <time> (0)
155 Only use frame when t MOD dt = first time (default unit ps)
156 -tu <enum> (ps)
158 Unit for time values: fs, ps, ns, us, ms, s
159 -[no]w (no)
161 View output .xvg, .xpm, .eps and .pdb files
162 -xvg <enum> (xmgrace)
164 xvg plot formatting: xmgrace, xmgr, none
165 -[no]dista (no)
167 Use RMSD of distances instead of RMS deviation
168 -nlevels <int> (40)
170 Discretize RMSD matrix in this number of levels
171 -cutoff <real> (0.1)
173 RMSD cut-off (nm) for two structures to be neighbor
174 -[no]fit (yes)
176 Use least squares fitting before RMSD calculation
177 -max <real> (-1)
179 Maximum level in RMSD matrix
180 -skip <int> (1)
182 Only analyze every nr-th frame
183 -[no]av (no)
185 Write average instead of middle structure for each cluster
186 -wcl <int> (0)
188 Write the structures for this number of clusters to numbered
189 files
190 -nst <int> (1)
192 Only write all structures if more than this number of structures
193 per cluster
194 -rmsmin <real> (0)
196 minimum rms difference with rest of cluster for writing struc‐
197 tures
198 -method <enum> (linkage)
200 Method for cluster determination: linkage, jarvis-patrick,
201 monte-carlo, diagonalization, gromos
202 -minstruct <int> (1)
204 Minimum number of structures in cluster for coloring in the .xpm
205 file
206 -[no]binary (no)
208 Treat the RMSD matrix as consisting of 0 and 1, where the
209 cut-off is given by -cutoff
210 -M <int> (10)
212 Number of nearest neighbors considered for Jarvis-Patrick algo‐
213 rithm, 0 is use cutoff
214 -P <int> (3)
216 Number of identical nearest neighbors required to form a cluster
217 -seed <int> (0)
219 Random number seed for Monte Carlo clustering algorithm (0 means
220 generate)
221 -niter <int> (10000)
223 Number of iterations for MC
224 -nrandom <int> (0)
226 The first iterations for MC may be done complete random, to
227 shuffle the frames
228 -kT <real> (0.001)
230 Boltzmann weighting factor for Monte Carlo optimization (zero
231 turns off uphill steps)
232 -[no]pbc (yes)
234 PBC check
235
237 gmx(1)
238 More information about GROMACS is available at <‐
240 http://www.gromacs.org/>.
241
243 2019, GROMACS development team
2442018.7 May 29, 2019 GMX-CLUSTER(1)