1GMX-CLUSTER(1)                      GROMACS                     GMX-CLUSTER(1)
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NAME

6       gmx-cluster - Cluster structures
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SYNOPSIS

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/...>]]
14                      [-clndx [<.ndx>]] [-b <time>] [-e <time>] [-dt <time>]
15                      [-tu <enum>] [-[no]w] [-xvg <enum>] [-[no]dista]
16                      [-nlevels <int>] [-cutoff <real>] [-[no]fit]
17                      [-max <real>] [-skip <int>] [-[no]av] [-wcl <int>]
18                      [-nst <int>] [-rmsmin <real>] [-method <enum>]
19                      [-minstruct <int>] [-[no]binary] [-M <int>] [-P <int>]
20                      [-seed <int>] [-niter <int>] [-nrandom <int>]
21                      [-kT <real>] [-[no]pbc]
22

DESCRIPTION

24       gmx  cluster  can  cluster  structures using several different methods.
25       Distances between structures can be determined  from  a  trajectory  or
26       read from an .xpm matrix file with the -dm option.  RMS deviation after
27       fitting or RMS deviation of atom-pair distances can be used  to  define
28       the distance between structures.
29
30       single  linkage:  add a structure to a cluster when its distance to any
31       element of the cluster is less than cutoff.
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33       Jarvis Patrick: add a structure to a cluster when this structure and  a
34       structure  in  the cluster have each other as neighbors and they have a
35       least P neighbors in common. The neighbors of a  structure  are  the  M
36       closest structures or all structures within cutoff.
37
38       Monte  Carlo:  reorder  the RMSD matrix using Monte Carlo such that the
39       order of the frames is using the smallest  possible  increments.   With
40       this it is possible to make a smooth animation going from one structure
41       to another with the largest possible (e.g.) RMSD between them,  however
42       the  intermediate  steps  should be as small as possible.  Applications
43       could be to visualize a potential of mean force ensemble of simulations
44       or  a pulling simulation. Obviously the user has to prepare the trajec‐
45       tory well (e.g. by not superimposing frames).  The final result can  be
46       inspect  visually by looking at the matrix .xpm file, which should vary
47       smoothly from bottom to top.
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49       diagonalization: diagonalize the RMSD matrix.
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51       gromos: use algorithm as described in Daura et al.  (Angew. Chem.  Int.
52       Ed.  1999,  38,  pp 236-240).  Count number of neighbors using cut-off,
53       take structure with largest number of neighbors with all its  neighbors
54       as  cluster  and eliminate it from the pool of clusters. Repeat for re‐
55       maining structures in pool.
56
57       When the clustering algorithm assigns each  structure  to  exactly  one
58       cluster  (single  linkage,  Jarvis Patrick and gromos) and a trajectory
59       file is supplied, the structure with the smallest average  distance  to
60       the  others or the average structure or all structures for each cluster
61       will be written to a trajectory file. When writing all structures, sep‐
62       arate numbered files are made for each cluster.
63
64       Two output files are always written:
65
66-o writes the RMSD values in the upper left half of the matrix and
67            a graphical depiction of the clusters in the lower right half When
68            -minstruct  =  1  the graphical depiction is black when two struc‐
69            tures are in the same cluster.  When -minstruct > 1 different col‐
70            ors will be used for each cluster.
71
72-g  writes  information on the options used and a detailed list of
73            all clusters and their members.
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75       Additionally, a number of optional output files can be written:
76
77-dist writes the RMSD distribution.
78
79-ev writes the eigenvectors of the RMSD matrix diagonalization.
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81-sz writes the cluster sizes.
82
83-tr writes a matrix of  the  number  transitions  between  cluster
84            pairs.
85
86-ntr  writes the total number of transitions to or from each clus‐
87            ter.
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89-clid writes the cluster number as a function of time.
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91-clndx writes the frame numbers corresponding to the  clusters  to
92            the specified index file to be read into trjconv.
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94-cl  writes average (with option -av) or central structure of each
95            cluster or writes numbered files with cluster members  for  a  se‐
96            lected  set  of  clusters  (with  option -wcl, depends on -nst and
97            -rmsmin). The center of a cluster is the structure with the small‐
98            est average RMSD from all other structures of the cluster.
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OPTIONS

101       Options to specify input files:
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103       -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
104              Trajectory: xtc trr cpt gro g96 pdb tng
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106       -s [<.tpr/.gro/...>] (topol.tpr)
107              Structure+mass(db): tpr gro g96 pdb brk ent
108
109       -n [<.ndx>] (index.ndx) (Optional)
110              Index file
111
112       -dm [<.xpm>] (rmsd.xpm) (Optional)
113              X PixMap compatible matrix file
114
115       Options to specify output files:
116
117       -om [<.xpm>] (rmsd-raw.xpm)
118              X PixMap compatible matrix file
119
120       -o [<.xpm>] (rmsd-clust.xpm)
121              X PixMap compatible matrix file
122
123       -g [<.log>] (cluster.log)
124              Log file
125
126       -dist [<.xvg>] (rmsd-dist.xvg) (Optional)
127              xvgr/xmgr file
128
129       -ev [<.xvg>] (rmsd-eig.xvg) (Optional)
130              xvgr/xmgr file
131
132       -conv [<.xvg>] (mc-conv.xvg) (Optional)
133              xvgr/xmgr file
134
135       -sz [<.xvg>] (clust-size.xvg) (Optional)
136              xvgr/xmgr file
137
138       -tr [<.xpm>] (clust-trans.xpm) (Optional)
139              X PixMap compatible matrix file
140
141       -ntr [<.xvg>] (clust-trans.xvg) (Optional)
142              xvgr/xmgr file
143
144       -clid [<.xvg>] (clust-id.xvg) (Optional)
145              xvgr/xmgr file
146
147       -cl [<.xtc/.trr/...>] (clusters.pdb) (Optional)
148              Trajectory: xtc trr cpt gro g96 pdb tng
149
150       -clndx [<.ndx>] (clusters.ndx) (Optional)
151              Index file
152
153       Other options:
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155       -b <time> (0)
156              Time of first frame to read from trajectory (default unit ps)
157
158       -e <time> (0)
159              Time of last frame to read from trajectory (default unit ps)
160
161       -dt <time> (0)
162              Only use frame when t MOD dt = first time (default unit ps)
163
164       -tu <enum> (ps)
165              Unit for time values: fs, ps, ns, us, ms, s
166
167       -[no]w (no)
168              View output .xvg, .xpm, .eps and .pdb files
169
170       -xvg <enum> (xmgrace)
171              xvg plot formatting: xmgrace, xmgr, none
172
173       -[no]dista (no)
174              Use RMSD of distances instead of RMS deviation
175
176       -nlevels <int> (40)
177              Discretize RMSD matrix in this number of levels
178
179       -cutoff <real> (0.1)
180              RMSD cut-off (nm) for two structures to be neighbor
181
182       -[no]fit (yes)
183              Use least squares fitting before RMSD calculation
184
185       -max <real> (-1)
186              Maximum level in RMSD matrix
187
188       -skip <int> (1)
189              Only analyze every nr-th frame
190
191       -[no]av (no)
192              Write average instead of middle structure for each cluster
193
194       -wcl <int> (0)
195              Write  the  structures  for  this number of clusters to numbered
196              files
197
198       -nst <int> (1)
199              Only write all structures if more than this number of structures
200              per cluster
201
202       -rmsmin <real> (0)
203              minimum  rms  difference with rest of cluster for writing struc‐
204              tures
205
206       -method <enum> (linkage)
207              Method  for  cluster  determination:  linkage,   jarvis-patrick,
208              monte-carlo, diagonalization, gromos
209
210       -minstruct <int> (1)
211              Minimum number of structures in cluster for coloring in the .xpm
212              file
213
214       -[no]binary (no)
215              Treat the RMSD matrix as  consisting  of  0  and  1,  where  the
216              cut-off is given by -cutoff
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218       -M <int> (10)
219              Number  of nearest neighbors considered for Jarvis-Patrick algo‐
220              rithm, 0 is use cutoff
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222       -P <int> (3)
223              Number of identical nearest neighbors required to form a cluster
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225       -seed <int> (0)
226              Random number seed for Monte Carlo clustering algorithm (0 means
227              generate)
228
229       -niter <int> (10000)
230              Number of iterations for MC
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232       -nrandom <int> (0)
233              The  first  iterations  for  MC  may be done complete random, to
234              shuffle the frames
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236       -kT <real> (0.001)
237              Boltzmann weighting factor for Monte  Carlo  optimization  (zero
238              turns off uphill steps)
239
240       -[no]pbc (yes)
241              PBC check
242

SEE ALSO

244       gmx(1)
245
246       More     information    about    GROMACS    is    available    at    <‐
247       http://www.gromacs.org/>.
248
250       2022, GROMACS development team
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2552022.2                           Jun 16, 2022                   GMX-CLUSTER(1)
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