PLUMED-NEST

Project ID: plumID:19.014
Source: mil-101_paper_setup/plumed_files/plumed_distances.dat
Originally used with PLUMED version: 2.2
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

RESTART
Activate restart. More details

The RESTART action with label  calculates something
DISTANCES
Calculate the distances between multiple piars of atoms This action is a shortcut. More details
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d1The DISTANCES action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
vector
the DISTANCES between the each pair of atoms that were specified
d1_lowest
scalar
the smallest of the colvars 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=1-3,61-63  
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=82,98,114,22,38,54 
LOWEST
 this flag allows you to recover the lowest of these variables
 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
# PLUMED interprets the command:
# DISTANCES LABEL=d1 GROUPA=1-3,61-63  GROUPB=82,98,114,22,38,54 LOWEST LOWMEM
# as follows (Click the red comment above to revert to the short version of the input):
d1_vatom1The CENTER_FAST action with label d1_vatom1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1_vatom1
atoms
virtual atom calculated by CENTER_FAST action: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=1,82
d1_vatom2The CENTER_FAST action with label d1_vatom2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1_vatom2
atoms
virtual atom calculated by CENTER_FAST action: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=1,98
d1_vatom3The CENTER_FAST action with label d1_vatom3 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1_vatom3
atoms
virtual atom calculated by CENTER_FAST action: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=1,114
d1_vatom4The CENTER_FAST action with label d1_vatom4 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1_vatom4
atoms
virtual atom calculated by CENTER_FAST action: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=1,22
d1_vatom5The CENTER_FAST action with label d1_vatom5 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1_vatom5
atoms
virtual atom calculated by CENTER_FAST action: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=1,38
d1_vatom6The CENTER_FAST action with label d1_vatom6 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1_vatom6
atoms
virtual atom calculated by CENTER_FAST action: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=1,54
# A further 36 CENTER like the ones above were also created but are not shown
d1_grpThe GROUP action with label d1_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
d1_grp
atoms
indices of atoms specified in GROUP: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=d1_vatom1,d1_vatom2,d1_vatom3,d1_vatom4,d1_vatom5,d1_vatom6,d1_vatom7,d1_vatom8,d1_vatom9,d1_vatom10,d1_vatom11,d1_vatom12,d1_vatom13,d1_vatom14,d1_vatom15,d1_vatom16,d1_vatom17,d1_vatom18,d1_vatom19,d1_vatom20,d1_vatom21,d1_vatom22,d1_vatom23,d1_vatom24,d1_vatom25,d1_vatom26,d1_vatom27,d1_vatom28,d1_vatom29,d1_vatom30,d1_vatom31,d1_vatom32,d1_vatom33,d1_vatom34,d1_vatom35,d1_vatom36
d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
vector
the DISTANCE for each set of specified atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS1
the pair of atom that we are calculating the distance between
=1,82 
ATOMS2
the pair of atom that we are calculating the distance between
=1,98 
ATOMS3
the pair of atom that we are calculating the distance between
=1,114 
ATOMS4
the pair of atom that we are calculating the distance between
=1,22 
ATOMS5
the pair of atom that we are calculating the distance between
=1,38     # Action input conctinues with 31 further ATOMSn keywords, 
d1_lowestThe LOWEST action with label d1_lowest calculates the following quantities:
 Quantity   
 Type   
 Description  
d1_lowest
scalar
the smallest element in the input vector if one vector specified.  If multiple vectors of the same size specified the largest elements of these vector computed elementwise.: 
LOWEST
This function can be used to find the lowest colvar by magnitude in a set. More details
 
ARG
the values input to this function
=d1
# --- End of included input --- 
DISTANCES
Calculate the distances between multiple piars of atoms This action is a shortcut. More details
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=d2The DISTANCES action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
vector
the DISTANCES between the each pair of atoms that were specified
d2_lowest
scalar
the smallest of the colvars 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=1-3        
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=61-63              
LOWEST
 this flag allows you to recover the lowest of these variables
 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
# PLUMED interprets the command:
# DISTANCES LABEL=d2 GROUPA=1-3        GROUPB=61-63              LOWEST LOWMEM
# as follows (Click the red comment above to revert to the short version of the input):
d2_vatom1The CENTER_FAST action with label d2_vatom1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2_vatom1
atoms
virtual atom calculated by CENTER_FAST action: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=1,61
d2_vatom2The CENTER_FAST action with label d2_vatom2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2_vatom2
atoms
virtual atom calculated by CENTER_FAST action: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=1,62
d2_vatom3The CENTER_FAST action with label d2_vatom3 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2_vatom3
atoms
virtual atom calculated by CENTER_FAST action: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=1,63
d2_vatom4The CENTER_FAST action with label d2_vatom4 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2_vatom4
atoms
virtual atom calculated by CENTER_FAST action: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=2,61
d2_vatom5The CENTER_FAST action with label d2_vatom5 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2_vatom5
atoms
virtual atom calculated by CENTER_FAST action: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=2,62
d2_vatom6The CENTER_FAST action with label d2_vatom6 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2_vatom6
atoms
virtual atom calculated by CENTER_FAST action: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=2,63
# A further 9 CENTER like the ones above were also created but are not shown
d2_grpThe GROUP action with label d2_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
d2_grp
atoms
indices of atoms specified in GROUP: 
GROUP
Define 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
 
ATOMS
the numerical indexes for the set of atoms in the group
=d2_vatom1,d2_vatom2,d2_vatom3,d2_vatom4,d2_vatom5,d2_vatom6,d2_vatom7,d2_vatom8,d2_vatom9
d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
vector
the DISTANCE for each set of specified atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS1
the pair of atom that we are calculating the distance between
=1,61 
ATOMS2
the pair of atom that we are calculating the distance between
=1,62 
ATOMS3
the pair of atom that we are calculating the distance between
=1,63 
ATOMS4
the pair of atom that we are calculating the distance between
=2,61 
ATOMS5
the pair of atom that we are calculating the distance between
=2,62     # Action input conctinues with 4 further ATOMSn keywords, 
d2_lowestThe LOWEST action with label d2_lowest calculates the following quantities:
 Quantity   
 Type   
 Description  
d2_lowest
scalar
the smallest element in the input vector if one vector specified.  If multiple vectors of the same size specified the largest elements of these vector computed elementwise.: 
LOWEST
This function can be used to find the lowest colvar by magnitude in a set. More details
 
ARG
the values input to this function
=d2
# --- End of included input --- 
METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
ARG
the labels of the scalars on which the bias will act
=d1.lowest,d2.lowest 
SIGMA
the widths of the Gaussian hills
=0.01,0.01 
HEIGHT
the heights of the Gaussian hills
=2.5
PACE
the frequency for hill addition
=500 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=298 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=30 
FILE
 a file in which the list of added hills is stored
=hills
GRID_MIN
the lower bounds for the grid
=-0.1,-0.1 
GRID_MAX
the upper bounds for the grid
=6.0,6.0     
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.005,0.005 
GRID_SPARSE
 use a sparse grid to store hills
... METAD

PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
ARG
the labels of the values that you would like to print to the file
=d1.lowest,d2.lowest,metad.bias 
FILE
the name of the file on which to output these quantities
=colvar

ENDPLUMED
Terminate plumed input. More details