PLUMED-NEST

Project ID: plumID:19.017
Source: plumed_metad/metad_20ang.dat
Originally used with PLUMED version: 2.5
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

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
=1-2593 
ENTITY1
the atoms that make up a molecule that you wish to align
=2594-2605
The WHOLEMOLECULES action with label  calculates something
FIT_TO_TEMPLATE
This action is used to align a molecule to a template. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=../input/heavy_atoms.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL

# Group definition
prot_nohThe GROUP action with label prot_noh calculates the following quantities:
 Quantity   
 Type   
 Description  
prot_noh
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
 
NDX_FILE
the name of index file (gromacs syntax)
=../input/index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Protein-H
sphThe GROUP action with label sph calculates the following quantities:
 Quantity   
 Type   
 Description  
sph
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
 
NDX_FILE
the name of index file (gromacs syntax)
=../input/index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=sphere
bnzThe GROUP action with label bnz calculates the following quantities:
 Quantity   
 Type   
 Description  
bnz
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
 
NDX_FILE
the name of index file (gromacs syntax)
=../input/index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=BNZ_noH

WRAPAROUND
Rebuild periodic boundary conditions around chosen atoms. More details
 
ATOMS
wrapped atoms
=bnz 
AROUND
reference atoms
=sph

sph_centerThe COM action with label sph_center calculates the following quantities:
 Quantity   
 Type   
 Description  
sph_center
atoms
virtual atom calculated by COM action: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=sph
bnz_centerThe COM action with label bnz_center calculates the following quantities:
 Quantity   
 Type   
 Description  
bnz_center
atoms
virtual atom calculated by COM action: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=bnz

sph_coordThe POSITION action with label sph_coord calculates the following quantities:
 Quantity   
 Type   
 Description  
sph_coord.x
scalar
the x-component of the atom position
sph_coord.y
scalar
the y-component of the atom position
sph_coord.z
scalar
the z-component of the atom position: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=sph_center 
NOPBC
 ignore the periodic boundary conditions when calculating distances
bnz_coordThe POSITION action with label bnz_coord calculates the following quantities:
 Quantity   
 Type   
 Description  
bnz_coord.x
scalar
the x-component of the atom position
bnz_coord.y
scalar
the y-component of the atom position
bnz_coord.z
scalar
the z-component of the atom position: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=bnz_center 
NOPBC
 ignore the periodic boundary conditions when calculating distances

abs_xThe MATHEVAL action with label abs_x calculates the following quantities:
 Quantity   
 Type   
 Description  
abs_x
scalar
an arbitrary function: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the values input to this function
=bnz_coord.x,sph_coord.x 
FUNC
the function you wish to evaluate
=x-y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
abs_yThe MATHEVAL action with label abs_y calculates the following quantities:
 Quantity   
 Type   
 Description  
abs_y
scalar
an arbitrary function: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the values input to this function
=bnz_coord.y,sph_coord.y 
FUNC
the function you wish to evaluate
=x-y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
abs_zThe MATHEVAL action with label abs_z calculates the following quantities:
 Quantity   
 Type   
 Description  
abs_z
scalar
an arbitrary function: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the values input to this function
=bnz_coord.z,sph_coord.z 
FUNC
the function you wish to evaluate
=x-y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

rhoThe MATHEVAL action with label rho calculates the following quantities:
 Quantity   
 Type   
 Description  
rho
scalar
an arbitrary function: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the values input to this function
=abs_x,abs_y,abs_z 
FUNC
the function you wish to evaluate
=sqrt(x*x+y*y+z*z 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
thetaThe MATHEVAL action with label theta calculates the following quantities:
 Quantity   
 Type   
 Description  
theta
scalar
an arbitrary function: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the values input to this function
=abs_z,rho 
FUNC
the function you wish to evaluate
=acos(x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=0.,pi
phiThe MATHEVAL action with label phi calculates the following quantities:
 Quantity   
 Type   
 Description  
phi
scalar
an arbitrary function: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the values input to this function
=abs_x,abs_y 
FUNC
the function you wish to evaluate
=atan2(y,x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=-pi,pi

# Restraining potential of the sphere
restrThe UPPER_WALLS action with label restr calculates the following quantities:
 Quantity   
 Type   
 Description  
restr.bias
scalar
the instantaneous value of the bias potential
restr.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=rho 
AT
the positions of the wall
=2.0 
KAPPA
the force constant for the wall
=10000

# Coordination number
cThe COORDINATION action with label c calculates the following quantities:
 Quantity   
 Type   
 Description  
c
scalar
the value of the coordination: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=bnz 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=prot_noh 
R_0
The r_0 parameter of the switching function
=0.45
c: 
COORDINATION
Calculate coordination numbers. This action uses the defaults shown here. More details
 
GROUPA
First list of atoms
=bnz 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=prot_noh 
R_0
The r_0 parameter of the switching function
=0.45  
D_0
 The d_0 parameter of the switching function
=0.0 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=0

# Metadynamics
METAD
Used to performed metadynamics on one or more collective variables. This action has hidden defaults. More details
 ...
ARG
the labels of the scalars on which the bias will act
=rho,theta,phi
GRID_MIN
the lower bounds for the grid
=0,0.,-pi
GRID_MAX
the upper bounds for the grid
=2.2,pi,pi
SIGMA
the widths of the Gaussian hills
=0.1,pi/16.,pi/8
HEIGHT
the heights of the Gaussian hills
=1.2
PACE
the frequency for hill addition
=500
BIASFACTOR
use well tempered metadynamics and use this bias factor
=20
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
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
metad.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
metad.rct
scalar
the reweighting factor c(t).
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... METAD
METAD
Used to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details
 ...
ARG
the labels of the scalars on which the bias will act
=rho,theta,phi
GRID_MIN
the lower bounds for the grid
=0,0.,-pi
GRID_MAX
the upper bounds for the grid
=2.2,pi,pi
SIGMA
the widths of the Gaussian hills
=0.1,pi/16.,pi/8
HEIGHT
the heights of the Gaussian hills
=1.2
PACE
the frequency for hill addition
=500
BIASFACTOR
use well tempered metadynamics and use this bias factor
=20
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
 
FILE
 a file in which the list of added hills is stored
=HILLS
... METAD


PRINT
Print quantities to a file. More details
 
ARG
the labels of the values that you would like to print to the file
=rho 
FILE
the name of the file on which to output these quantities
=distance.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the labels of the values that you would like to print to the file
=metad 
FILE
the name of the file on which to output these quantities
=metad_data.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the labels of the values that you would like to print to the file
=restr 
FILE
the name of the file on which to output these quantities
=sphere_restraint.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the labels of the values that you would like to print to the file
=abs_x,abs_y,abs_z 
FILE
the name of the file on which to output these quantities
=xyz_coord.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the labels of the values that you would like to print to the file
=rho,theta,phi 
FILE
the name of the file on which to output these quantities
=rtp_coord.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the labels of the values that you would like to print to the file
=c 
FILE
the name of the file on which to output these quantities
=all_coordination_45.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=500

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
=500