PLUMED-NEST-TEST-SITE

Project ID: plumID:24.006
Source: clusterFormationFreeEnergy/plumed.dat
Originally used with PLUMED version: 2.8
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=ps ENERGYthe units of energy=eV  #KB=1.380649e-23 J/K 
The UNITS action with label  calculates somethingc1: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-300:3 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1 D_0=3.5 D_MAX=4.5} LOWMEM this flag does nothing and is present only to ensure back-compatibility
The COORDINATIONNUMBER action with label c1 calculates the following quantities:
 Quantity   
 Description  
c1.value
the coordination numbers of the specified atomsmat: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details ATOMSthe atoms for which you would like to calculate the adjacency matrix=c1 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1 D_0=3.5 D_MAX=4.5}
The CONTACT_MATRIX action with label mat calculates the following quantities:
 Quantity   
 Description  
mat.value
a matrix containing the weights for the bonds between each pair of atomsdfs: DFSCLUSTERINGFind the connected components of the matrix using the depth first search clustering algorithm. More details MATRIXthe input matrix (can use ARG instead)=mat LOWMEM this flag does nothing and is present only to ensure back-compatibility
The DFSCLUSTERING action with label dfs calculates the following quantities:
 Quantity   
 Description  
dfs.value
vector with length that is equal to the number of rows in the input matrixclust1: CLUSTER_PROPERTIESCalculate properties of the distribution of some quantities that are part of a connected component More details CLUSTERSthe label of the action that does the clustering=dfs CLUSTER which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on=1 SUM calculate the sum of all the quantities LOWMEM 
The CLUSTER_PROPERTIES action with label clust1 calculates the following quantities:
 Quantity   
 Description  
clust1.value
a vector that is one if the atom is part of the cluster or interest and zero otherwise
clust1.sum
the sum of the colvarsnat: CLUSTER_NATOMSCalculate the number of atoms in the cluster of interest More details CLUSTERSthe label of the action that does the clustering=dfs CLUSTER which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on=1  
The CLUSTER_NATOMS action with label nat calculates the following quantities:
 Quantity   
 Description  
nat.value
the number of atoms in the clustermt: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=clust1.sum ...
 PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=0.02 BIASFACTORuse well tempered metadynamics and use this bias factor=50   
 SIGMAthe widths of the Gaussian hills=1 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=373  
 FILE a file in which the list of added hills is stored=HILLS GRID_MINthe lower bounds for the grid=0 GRID_MAXthe upper bounds for the grid=500 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
...

The METAD action with label mt calculates the following quantities:
 Quantity   
 Description  
mt.bias
the instantaneous value of the bias potential
mt.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
mt.rct
the reweighting factor c(t)UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=clust1.sum ATthe positions of the wall=250.0 KAPPAthe force constant for the wall=0.1 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=uwall 
The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentialPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=500