PLUMED-NEST

Project ID: plumID:19.026
Source: EXAMPLE/plumed.dat
Originally used with PLUMED version: 2.3.0-mod
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

# Order parameter:
# Number of water molecules within the largest connected "icy" cluster
# Whether a water molecule is defined as icy or not, it depends on its hydrogen bond network
# as well as the value of an order parameter built on the Steinhardt parameter Q6.
# The exact definition can be found at:
# https://pubs.acs.org/doi/suppl/10.1021/acs.jpclett.6b01013/suppl_file/jz6b01013_si_001.pdf

# Geometric criteria for hydrogen bonds (HBs) 
HBOND_COORDThis action is not part of PLUMED and was included by using a LOAD command More details SPECIES=2665-10353:4 HYDROGENS=2666-10354:4,2667-10355:4 RCUTOO=0.324 RCUTOH=0.25 ACUT=0.20pi LABEL=hb

# Selecting those oxygens with 4 HB
MFILTER_BETWEENThis action is not part of PLUMED and was included by using a LOAD command More details DATA=hb LOWER=3.9 UPPER=4.1 SMEAR=0.0 LABEL=rsumsb

# Steinhardt parameter Q6 for this particular subset of molecules 
Q6Calculate sixth order Steinhardt parameters. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=rsumsb                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.={GAUSSIAN D_0=0.324  R_0=0.00001 D_MAX=0.3241} LABELa label for the action so that its output can be referenced in the input to other actions=q6 LOWMEM this flag does nothing and is present only to ensure back-compatibility

# Local Q6 (see Plumed Docs, LOCAL_Q6) for this particular subset
The Q6 action with label q6 calculates the following quantities:
 Quantity   
 Description  
q6.value
the norms of the vectors of spherical harmonic coefficientsLOCAL_Q6Calculate the local degree of order around an atoms by taking the average dot product between the q_6 vector on the central atom and the q_6 vector on the atoms in the first coordination sphere. More details DATA=q6                 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={GAUSSIAN D_0=0.324  R_0=0.00001 D_MAX=0.3241} LABELa label for the action so that its output can be referenced in the input to other actions=lq6 LOWMEM this flag does nothing and is present only to ensure back-compatibility

# Selecting atoms with a certain value of LQ6
The LOCAL_Q6 action with label lq6 calculates the following quantities:
 Quantity   
 Description  
lq6.value
the values of the local steinhardt parameters for the input atomsMFILTER_MOREApply one minus a switching function to the input vector. More details DATAthe vector you wish to transform=lq6            SWITCHthe switching function that transform={GAUSSIAN D_0=0.45   R_0=0.00001 D_MAX=0.4501} LABELa label for the action so that its output can be referenced in the input to other actions=cf

# Create a contact matrix based on distance
The MFILTER_MORE action with label cf calculates the following quantities:
 Quantity   
 Description  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=cf WTOL=0.1 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.={GAUSSIAN D_0=0.324  R_0=0.00001 D_MAX=0.3241} LABELa label for the action so that its output can be referenced in the input to other actions=mat

# Clustering, based on MFILTER_MORE and CONTACT_MATRIX
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 atomsDFSCLUSTERINGFind the connected components of the matrix using the depth first search clustering algorithm. More details MATRIXthe input matrix (can use ARG instead)=mat LABELa label for the action so that its output can be referenced in the input to other actions=cls SERIAL

# Including "surface" (nearest neighbours) atoms
The DFSCLUSTERING action with label cls calculates the following quantities:
 Quantity   
 Description  
cls.value
vector with length that is equal to the number of rows in the input matrixCLUSTER_WITHSURFACEDetermine the atoms that are within a certain cutoff of the atoms in a cluster. More details CLUSTERSthe label of the action that does the clustering=cls RCUT_SURFthe cutoff to use for determining which atoms are connected to the surface of the cluster=0.324 LABELa label for the action so that its output can be referenced in the input to other actions=scls SERIAL

# Finding the largest connected cluster - this is the order parameter lambda we are building our
# Forward Flux Sampling (FFS) machinery upon
The CLUSTER_WITHSURFACE action with label scls calculates the following quantities:
 Quantity   
 Description  
scls.value
a vector that is one for those atoms that are within the cluster or that are within a cetain cutoff of one of the atoms in the cluster and zero otherwiseCLUSTER_NATOMSCalculate the number of atoms in the cluster of interest More details CLUSTERSthe label of the action that does the clustering=scls 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 LABELa label for the action so that its output can be referenced in the input to other actions=lambda

# In order to decide whether a particular MD run has reached the next FFS interface 
# (see e.g. https://pubs.acs.org/doi/abs/10.1021/acs.jpclett.6b01013) or got back to the first interface,
# we use the COMMITTOR action
The CLUSTER_NATOMS action with label lambda calculates the following quantities:
 Quantity   
 Description  
lambda.value
the number of atoms in the clusterCOMMITTORDoes a committor analysis. More details ARGthe labels of the values which is being used to define the committor surface=lambda STRIDE the frequency with which the CVs are analyzed=2000 BASIN_LL1List of lower limits for basin #=0 BASIN_UL1List of upper limits for basin #=24 BASIN_LL2List of lower limits for basin #=110 BASIN_UL2List of upper limits for basin #=10000 FILEthe name of the file on which to output the reached basin=shoot.dat

# Output the value of lambda as we go along
The COMMITTOR action with label  calculates somethingOUTPUT_CLUSTEROutput the indices of the atoms in one of the clusters identified by a clustering object More details CLUSTERSthe action that performed the clustering=scls 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 STRIDE the frequency with which you would like to output the atoms in the cluster=2000 FILEthe name of the file on which to output the details of the cluster=dfs_surf.dat # Output lambda
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=2000

ENDPLUMEDTerminate plumed input. More details