PLUMED-NEST

Project ID: plumID:21.011
Source: NaCl_at_graphite-cmumd/coordination-profiles.plmd
Originally used with PLUMED version: 2.5.1
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

# Define atom groups
gra: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-9152:1 
The GROUP action with label gra calculates somethingwat: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=9153-43319:3
The GROUP action with label wat calculates somethingsod: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=43320-43737:1
The GROUP action with label sod calculates somethingchl: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=43738-44155:1
The GROUP action with label chl calculates somethingslt: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=43320-44155:1
The GROUP action with label slt calculates somethingsln: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=9153-44155:1 

# Set a virtual atom at the origin and in the 'bulk'
The GROUP action with label sln calculates somethingp0: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.696525,2.75872,7.403535
The FIXEDATOM action with label p0 calculates somethingp1: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.696525,2.75872,11.403535

# Get the coordination number distributions
The FIXEDATOM action with label p1 calculates somethingcn0:  COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthis keyword is used for colvars such as the coordination number=sod SPECIESBthis keyword is used for colvars such as the coordination number=chl SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=0.355 NN=32 MM=64}
The COORDINATIONNUMBER action with label cn0 calculates the following quantities:
 Quantity   
 Description  
cn0.value
the coordination numbers of the specified atomscn1:  COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthis keyword is used for colvars such as the coordination number=sod SPECIESBthis keyword is used for colvars such as the coordination number=wat SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=0.325 NN=32 MM=64}
The COORDINATIONNUMBER action with label cn1 calculates the following quantities:
 Quantity   
 Description  
cn1.value
the coordination numbers of the specified atomscn2:  COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthis keyword is used for colvars such as the coordination number=chl SPECIESBthis keyword is used for colvars such as the coordination number=wat SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=0.385 NN=32 MM=64}
The COORDINATIONNUMBER action with label cn2 calculates the following quantities:
 Quantity   
 Description  
cn2.value
the coordination numbers of the specified atomscn3:  COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthis keyword is used for colvars such as the coordination number=sod SPECIESBthis keyword is used for colvars such as the coordination number=gra SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=0.365 NN=32 MM=64}
The COORDINATIONNUMBER action with label cn3 calculates the following quantities:
 Quantity   
 Description  
cn3.value
the coordination numbers of the specified atomsips: MFILTER_MOREBasically equivalent to MORE_THAN. More details DATAthe vector you wish to transform=cn0 SWITCHthe switching function that transform={GAUSSIAN D_0=0.9999 R_0=0.00001}

The MFILTER_MORE action with label ips calculates the following quantities:
 Quantity   
 Description  densnacl: MULTICOLVARDENSEvaluate the average value of a multicolvar on a grid. More details DATAthe multicolvar which you would like to calculate the density profile for=cn0 ORIGINwe will use the position of this atom as the origin=p0 DIRthe direction in which to calculate the density profile=z NBINSthe number of bins to use in each direction (alternative to GRID_NBIN)=1480 KERNEL the kernel function you are using=GAUSSIAN BANDWIDTHthe bandwidths for kernel density esimtation=0.03 NORMALIZATIONset true/false to determine how to the data is normalised=true STRIDE the frequency with which to accumulate the densities=1
The MULTICOLVARDENS action with label densnacl calculates the following quantities:
 Quantity   
 Description  
densnacl.value
the average value of the order parameters at each point on the griddensnaow: MULTICOLVARDENSEvaluate the average value of a multicolvar on a grid. More details DATAthe multicolvar which you would like to calculate the density profile for=cn1 ORIGINwe will use the position of this atom as the origin=p0 DIRthe direction in which to calculate the density profile=z NBINSthe number of bins to use in each direction (alternative to GRID_NBIN)=1480 KERNEL the kernel function you are using=GAUSSIAN BANDWIDTHthe bandwidths for kernel density esimtation=0.03 NORMALIZATIONset true/false to determine how to the data is normalised=true STRIDE the frequency with which to accumulate the densities=1
The MULTICOLVARDENS action with label densnaow calculates the following quantities:
 Quantity   
 Description  
densnaow.value
the average value of the order parameters at each point on the griddensclow: MULTICOLVARDENSEvaluate the average value of a multicolvar on a grid. More details DATAthe multicolvar which you would like to calculate the density profile for=cn2 ORIGINwe will use the position of this atom as the origin=p0 DIRthe direction in which to calculate the density profile=z NBINSthe number of bins to use in each direction (alternative to GRID_NBIN)=1480 KERNEL the kernel function you are using=GAUSSIAN BANDWIDTHthe bandwidths for kernel density esimtation=0.03 NORMALIZATIONset true/false to determine how to the data is normalised=true STRIDE the frequency with which to accumulate the densities=1
The MULTICOLVARDENS action with label densclow calculates the following quantities:
 Quantity   
 Description  
densclow.value
the average value of the order parameters at each point on the griddensnagra: MULTICOLVARDENSEvaluate the average value of a multicolvar on a grid. More details DATAthe multicolvar which you would like to calculate the density profile for=cn3 ORIGINwe will use the position of this atom as the origin=p0 DIRthe direction in which to calculate the density profile=z NBINSthe number of bins to use in each direction (alternative to GRID_NBIN)=1480 KERNEL the kernel function you are using=GAUSSIAN BANDWIDTHthe bandwidths for kernel density esimtation=0.03 NORMALIZATIONset true/false to determine how to the data is normalised=true STRIDE the frequency with which to accumulate the densities=1
The MULTICOLVARDENS action with label densnagra calculates the following quantities:
 Quantity   
 Description  
densnagra.value
the average value of the order parameters at each point on the griddensips: MULTICOLVARDENSEvaluate the average value of a multicolvar on a grid. More details DATAthe multicolvar which you would like to calculate the density profile for=ips ORIGINwe will use the position of this atom as the origin=p0 DIRthe direction in which to calculate the density profile=z NBINSthe number of bins to use in each direction (alternative to GRID_NBIN)=1480 KERNEL the kernel function you are using=GAUSSIAN BANDWIDTHthe bandwidths for kernel density esimtation=0.03 NORMALIZATIONset true/false to determine how to the data is normalised=true STRIDE the frequency with which to accumulate the densities=1

The MULTICOLVARDENS action with label densips calculates the following quantities:
 Quantity   
 Description  
densips.value
the average value of the order parameters at each point on the gridDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=densnacl FILE the file on which to write the grid=DENSna-cl.dat
The DUMPGRID action with label  calculates somethingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=densnaow FILE the file on which to write the grid=DENSna-ow.dat
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=densclow FILE the file on which to write the grid=DENScl-ow.dat
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=densnagra FILE the file on which to write the grid=DENSna-gra.dat
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=densips FILE the file on which to write the grid=DENSips.dat