PLUMED-NEST

Project ID: plumID:22.016
Source: SurfaceFreeEnergy/Basal/plumed.dat
Originally used with PLUMED version: 2.8
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
Activate restart. More details

ENVIRONMENTSIMILARITY
Measure how similar the environment around atoms is to that found in some reference crystal structure. More details
 ...
 
SPECIES
this keyword is used for colvars such as coordination number
=1-1728:3
 
SIGMA
 the width to use for the gaussian kernels
=0.0675
 
CRYSTAL_STRUCTURE
 Targeted crystal structure
=CUSTOM
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=refcv
 
REFERENCE_1
PDB files with relative distances from central atom
=env1h.pdb
 
REFERENCE_2
PDB files with relative distances from central atom
=env2h.pdb
 
REFERENCE_3
PDB files with relative distances from central atom
=env3h.pdb
 
REFERENCE_4
PDB files with relative distances from central atom
=env4h.pdb
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={CUBIC D_0=0.60 D_MAX=0.98}
 
MEAN
 calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY

s: 
AROUND
This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. More details
 
DATA
the label of an action that calculates multicolvars
=refcv 
ATOM
an alternative to ORIGIN
=1 
ZLOWER
 the lower boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box)
=-0.5 
ZUPPER
 the upper boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box)
=0.5 
SIGMA
the width of the function to be used for kernel density estimation
=0.03 
MEAN
 calculate the average value of the colvar inside the region of interest
 
MORE_THAN
calcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold
={CUBIC D_0=0.60 D_MAX=0.98}

The AROUND action with label s calculates the following quantities:
 Quantity   
 Description  
s.morethan
the number of cvs in the region of interest that are more than a certain threshold
s.mean
the average values of the colvar in the region of interest
ENVIRONMENTSIMILARITY
Measure how similar the environment around atoms is to that found in some reference crystal structure. More details
 ...
 
SPECIESA
this keyword is used for colvars such as the coordination number
=1
 
SPECIESB
this keyword is used for colvars such as the coordination number
=4-1728:3
 
SIGMA
 the width to use for the gaussian kernels
=0.0675
 
CRYSTAL_STRUCTURE
 Targeted crystal structure
=CUSTOM
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=refcv2
 
REFERENCE_1
PDB files with relative distances from central atom
=env1h.pdb
 
REFERENCE_2
PDB files with relative distances from central atom
=env2h.pdb
 
REFERENCE_3
PDB files with relative distances from central atom
=env3h.pdb
 
REFERENCE_4
PDB files with relative distances from central atom
=env4h.pdb
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={CUBIC D_0=0.60 D_MAX=0.98}
 
MEAN
 calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY

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

The VOLUME action with label vol calculates a scalar quantity
OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=s.morethan,refcv2.morethan 
PACE
the frequency for kernel deposition
=500 
STRIDE
the frequency with which the forces due to the bias should be calculated
=2 
TEMP
 temperature
=312 
BARRIER
the free energy barrier to be overcome
=350 
WALKERS_MPI
 switch on MPI version of multiple walkers
 

The OPES_METAD action with label  calculates the following quantities:
 Quantity   
 Description  
.bias
the instantaneous value of the bias potential
.rct
estimate of c(t)
.zed
estimate of Z_n
.neff
effective sample size
.nker
total number of compressed kernels used to represent the bias
ENVIRONMENTSIMILARITY
Measure how similar the environment around atoms is to that found in some reference crystal structure. More details
 ...
 
SPECIES
this keyword is used for colvars such as coordination number
=1-1728:3
 
SIGMA
 the width to use for the gaussian kernels
=0.08
 
CRYSTAL_STRUCTURE
 Targeted crystal structure
=CUSTOM
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=refcv3
 
REFERENCE_1
PDB files with relative distances from central atom
=env1c.pdb
 
REFERENCE_2
PDB files with relative distances from central atom
=env2c.pdb
 
REFERENCE_3
PDB files with relative distances from central atom
=env3c.pdb
 
REFERENCE_4
PDB files with relative distances from central atom
=env4c.pdb
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={CUBIC D_0=1.00 D_MAX=1.13}
 
MEAN
 calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY

diff: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=refcv.morethan,s.morethan 
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

uwall1: 
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
=diff 
AT
the positions of the wall
=50 
KAPPA
the force constant for the wall
=1.0 
EXP
 the powers for the walls
=2 
STRIDE
the frequency with which the forces due to the bias should be calculated
=2
uwall2: 
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
=refcv3.morethan 
AT
the positions of the wall
=0 
KAPPA
the force constant for the wall
=20.0 
EXP
 the powers for the walls
=2 
STRIDE
the frequency with which the forces due to the bias should be calculated
=4

diff2: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=s.morethan,refcv2.morethan 
FUNC
the function you wish to evaluate
=x/144-y/0.9 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
uwall3: 
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
=diff2 
AT
the positions of the wall
=0 
KAPPA
the force constant for the wall
=4000.0 
EXP
 the powers for the walls
=2 
STRIDE
the frequency with which the forces due to the bias should be calculated
=2

ENVIRONMENTSIMILARITY
Measure how similar the environment around atoms is to that found in some reference crystal structure. More details
 ...
 
SPECIES
this keyword is used for colvars such as coordination number
=1-1728:3
 
SIGMA
 the width to use for the gaussian kernels
=0.065
 
CRYSTAL_STRUCTURE
 Targeted crystal structure
=CUSTOM
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=refcv4
 
REFERENCE_1
PDB files with relative distances from central atom
=Large/env1h.pdb
 
REFERENCE_2
PDB files with relative distances from central atom
=Large/env2h.pdb
 
REFERENCE_3
PDB files with relative distances from central atom
=Large/env3h.pdb
 
REFERENCE_4
PDB files with relative distances from central atom
=Large/env4h.pdb
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={CUBIC D_0=0.65 D_MAX=0.67}
 
MEAN
 calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY

s2: 
AROUND
This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. More details
 
DATA
the label of an action that calculates multicolvars
=refcv4 
ATOM
an alternative to ORIGIN
=1 
ZLOWER
 the lower boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box)
=-0.14 
ZUPPER
 the upper boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box)
=0.14 
SIGMA
the width of the function to be used for kernel density estimation
=0.001 
MEAN
 calculate the average value of the colvar inside the region of interest
 
MORE_THAN
calcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold
={CUBIC D_0=0.65 D_MAX=0.67}

The AROUND action with label s2 calculates the following quantities:
 Quantity   
 Description  
s2.morethan
the number of cvs in the region of interest that are more than a certain threshold
s2.mean
the average values of the colvar in the region of interest
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=500  
ARG
the input for this action is the scalar output from one or more other actions
 
FILE
the name of the file on which to output these quantities
=COLVAR