PLUMED-NEST

Project ID: plumID:22.002
Source: OAH-G4/plumed.dat
Originally used with PLUMED version: 2.6
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=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 
#RESTART
LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=GAMBES_log_static_few.cpp #GAMBES_log.cpp
#LOAD FILE=GAMBES_test1.cpp
#LIGAND/HOST
CAL: 
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
=29-212

#GUEST
GC: 
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
=1-11
GO: 
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
=12-13
GBr: 
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
=14
GSEL: 
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
=2,3,11,14
l1: 
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
=2
l2: 
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
=3
l3: 
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
=11
l4: 
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
=14

#Water
WO: 
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
=222-6521:3

WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=CAL
FIT_TO_TEMPLATE
This action is used to align a molecule to a template. More details
 
STRIDE
 the frequency with which molecules are reassembled
=1 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=conf_template.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL
lig: 
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
=GC  #check
pock: 
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
=29-68
##DISTANCE ATOMS=pock,lig LABEL=d1  COMPONENTS 

v1: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=2.0136,2.0136,2.0
v2: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=2.0136,2.0136,2.25
v3: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=2.0136,2.0136,2.5
v4: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=2.0136,2.0136,2.75
v5: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=2.0136,2.0136,3.0
v6: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=2.0136,2.0136,3.25
v7: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=2.0136,2.0136,3.5
v8: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=2.0136,2.0136,3.75
VIRT: 
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
=v1,v2,v3,v4,v5,v6,v7,v8

cyl: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=v1,lig 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
  #NEW DISTANCE

The DISTANCE action with label cyl calculates the following quantities:
 Quantity   
 Description  
cyl.x
the x-component of the vector connecting the two atoms
cyl.y
the y-component of the vector connecting the two atoms
cyl.z
the z-component of the vector connecting the two atomscswo1: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=l1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=1.0 NOSTRETCH} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.4 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5
The COORDINATION action with label cswo1 calculates a scalar quantitycswo2: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=l2 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=1.0 NOSTRETCH} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.4 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5
The COORDINATION action with label cswo2 calculates a scalar quantitycswo3: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=l3 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=1.0 NOSTRETCH} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.4 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5
The COORDINATION action with label cswo3 calculates a scalar quantitycswo4: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=l4 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=1.0 NOSTRETCH} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.4 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5
The COORDINATION action with label cswo4 calculates a scalar quantitycvwo1: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=v1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.4 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5
The COORDINATION action with label cvwo1 calculates a scalar quantitycvwo2: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=v2 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.4 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5
The COORDINATION action with label cvwo2 calculates a scalar quantitycvwo3: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=v3 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.4 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5
The COORDINATION action with label cvwo3 calculates a scalar quantitycvwo4: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=v4 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.4 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5
The COORDINATION action with label cvwo4 calculates a scalar quantitycvwo5: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=v5 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.4 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5
The COORDINATION action with label cvwo5 calculates a scalar quantitycvwo6: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=v6 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.4 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5
The COORDINATION action with label cvwo6 calculates a scalar quantitycvwo7: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=v7 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.4 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5
The COORDINATION action with label cvwo7 calculates a scalar quantitycvwo8: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=v8 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.4 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5

The COORDINATION action with label cvwo8 calculates a scalar quantityd1: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=cswo1 
FUNC
the function you wish to evaluate
=(x/2.5)-1.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
d2: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=cswo2 
FUNC
the function you wish to evaluate
=(x/2.5)-1.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
d3: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=cswo3 
FUNC
the function you wish to evaluate
=(x/2.5)-1.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
d4: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=cswo4 
FUNC
the function you wish to evaluate
=(x/2.5)-1.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
d5: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=cvwo1 
FUNC
the function you wish to evaluate
=(x/2.8)-1.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
d6: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=cvwo2 
FUNC
the function you wish to evaluate
=(x/2.8)-1.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
d7: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=cvwo3 
FUNC
the function you wish to evaluate
=(x/2.8)-1.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
d8: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=cvwo4 
FUNC
the function you wish to evaluate
=(x/2.8)-1.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
d9: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=cvwo5 
FUNC
the function you wish to evaluate
=(x/2.8)-1.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
d10: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=cvwo6 
FUNC
the function you wish to evaluate
=(x/2.8)-1.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
d11: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=cvwo7 
FUNC
the function you wish to evaluate
=(x/2.8)-1.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
d12: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=cvwo8 
FUNC
the function you wish to evaluate
=(x/2.8)-1.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
################################

#NEW ANGLE
angcalg: 
ANGLE
Calculate an angle. More details
 
ATOMS
the list of atoms involved in this collective variable (either 3 or 4 atoms)
=v3,v5,6,11
The ANGLE action with label angcalg calculates a scalar quantitysang: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=angcalg 
FUNC
the function you wish to evaluate
=sin(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
cang: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=angcalg 
FUNC
the function you wish to evaluate
=cos(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

#Funnel
radius: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=cyl.x,cyl.y 
VAR
the names to give each of the arguments in the function
=x,y 
FUNC
the function you wish to evaluate
=sqrt(x*x+y*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
funnel: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=radius,cyl.z 
VAR
the names to give each of the arguments in the function
=r,z 
FUNC
the function you wish to evaluate
=(r+1.0*(-1.2+z))*step(-z+1.)+(r-0.2)*step(z-1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
AT
the positions of the wall
=0 
ARG
the arguments on which the bias is acting
=funnel 
KAPPA
the force constant for the wall
=2000.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=funnelwall

# Wall on distance to prevent the protein breaking
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
AT
the positions of the wall
=1.8 
ARG
the arguments on which the bias is acting
=cyl.z 
KAPPA
the force constant for the wall
=4000.0 
EXP
 the powers for the walls
=2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=upper_wall

autoA: 
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
 
FILE
Filename of the PyTorch compiled model
=modelG4_OAH_UW_OW1a.pt 
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12
The PYTORCH_MODEL action with label autoA calculates the following quantities:
 Quantity   
 Description  
autoA.node
Model outputsautoB: 
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
 
FILE
Filename of the PyTorch compiled model
=modelG4_OAH_UW_OW1b.pt 
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12
The PYTORCH_MODEL action with label autoB calculates the following quantities:
 Quantity   
 Description  
autoB.node
Model outputsautoC: 
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
 
FILE
Filename of the PyTorch compiled model
=modelG4_OAH_UW_OW1c.pt 
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12

The PYTORCH_MODEL action with label autoC calculates the following quantities:
 Quantity   
 Description  
autoC.node
Model outputsAcube: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=autoA.node-0 
FUNC
the function you wish to evaluate
=x+x^3 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
Bcube: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=autoB.node-0 
FUNC
the function you wish to evaluate
=x+x^3 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
Ccube: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=autoC.node-0 
FUNC
the function you wish to evaluate
=x+x^3 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

ene: 
ENERGY
Calculate the total potential energy of the simulation box. More details

cbhak: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=v1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.35 NN=16 MM=32} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5 

################################
The COORDINATION action with label cbhak calculates a scalar quantity
GAMBESL
This action is not part of PLUMED and was included by using a LOAD command More details
 ...
  LABEL=gambes
  NSTATES=3
  ARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,cyl.z
  PACE=500
  FILENAME=nstate
  BIAS_CUTOFF
  CUTOFF=110
#  STATIC_BIAS_OPTIMIZE
#  STATIC_FACTORS=1,0.28,-1
   STATIC_BIAS
   STATIC_FACTORS=1,0.28,0.5
... GAMBESL


#
#PRINT ARG=autoA.node-0,autoB.node-0,cvwo2,cyl.z,cvwo3,autoC.node-0,funnelwall.bias,upper_wall.bias,cvwo1,sang,cang,radius,Acube,Bcube,Ccube,cbhak,cswo1,cswo2,cswo3,cswo4,cvwo7,ene STRIDE=250 FILE=COLVARmeta FMT=%8.4f
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
 
STRIDE
 the frequency with which the quantities of interest should be output
=250 
FILE
the name of the file on which to output these quantities
=COLVAR 
FMT
the format that should be used to output real numbers
=%8.4f
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,cyl.z,cbhak,ene,gambes.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=250 
FILE
the name of the file on which to output these quantities
=COLVARNN 
FMT
the format that should be used to output real numbers
=%8.9f  
#PRINT ARG=radius,cyl.z STRIDE=250 FILE=COLVARbuca FMT=%8.4f
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cyl.z,Acube,gambes 
STRIDE
 the frequency with which the quantities of interest should be output
=250 
FILE
the name of the file on which to output these quantities
=col_desc 
FMT
the format that should be used to output real numbers
=%8.9f
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
=10

ENDPLUMED
Terminate plumed input. More details