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
tested onv2.9
tested onmaster
# 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_COORD
This 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_BETWEEN
This 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 

Q6
Calculate sixth order Steinhardt parameters. More details
 
SPECIES
this keyword is used for colvars such as coordination number
=rsumsb                
SWITCH
the switching function that it used in the construction of the contact matrix
={GAUSSIAN D_0=0.324  R_0=0.00001 D_MAX=0.3241} 
LABEL
a 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

LOCAL_Q6
Calculate 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                 
SWITCH
This 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} 
LABEL
a 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

MFILTER_MORE
Basically equivalent to MORE_THAN. More details
 
DATA
the vector you wish to transform
=lq6            
SWITCH
the switching function that transform
={GAUSSIAN D_0=0.45   R_0=0.00001 D_MAX=0.4501} 
LABEL
a 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

CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
ATOMS
the atoms for which you would like to calculate the adjacency matrix (basically equivalent to GROUP)
=cf WTOL=0.1 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={GAUSSIAN D_0=0.324  R_0=0.00001 D_MAX=0.3241} 
LABEL
a 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

DFSCLUSTERING
Find the connected components of the matrix using the depth first search clustering algorithm. More details
 
MATRIX
the input matrix (can use ARG instead)
=mat 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cls SERIAL

# Including "surface" (nearest neighbours) atoms

CLUSTER_WITHSURFACE
Determine the atoms that are within a certain cutoff of the atoms in a cluster More details
 
CLUSTERS
the label of the action that does the clustering
=cls RCUT_SURF=0.324 
LABEL
a 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

CLUSTER_NATOMS
Calculate the number of atoms in the cluster of interest More details
 
CLUSTERS
the 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 
LABEL
a 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

COMMITTOR
Does a committor analysis. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=lambda 
STRIDE
 the frequency with which the CVs are analyzed
=2000 
BASIN_LL1
List of lower limits for basin #
=0 
BASIN_UL1
List of upper limits for basin #
=24 
BASIN_LL2
List of lower limits for basin #
=110 
BASIN_UL2
List of upper limits for basin #
=10000 
FILE
the name of the file on which to output the reached basin
=shoot.dat

# Output the value of lambda as we go along

OUTPUT_CLUSTER
Output the indices of the atoms in one of the clusters identified by a clustering object More details
 
CLUSTERS
the 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 
FILE
the name of the file on which to output the details of the cluster
=dfs_surf.dat # Output lambda

FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=2000

ENDPLUMED
Terminate plumed input. More details