PLUMED-NEST

Project ID: plumID:23.028
Source: AIMD_simulation/plumed.dat
Originally used with PLUMED version: 2.9
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
UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A
The UNITS action with label  calculates somethingH: 
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
=9,10,11,12,13,14,15,16,27,28,31,32,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,147,148,149,150,155,156,157,158,161,162,167,168,169,170,175,176,177,178,181,182,183,184,189,190,191,192,197,198,258,259,260
The GROUP action with label H calculates somethingN: 
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
=17,18,19,20,21,22,23,24,25,26,29,30,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,151,152,153,154,159,160,163,164,165,166,171,172,173,174,179,180,185,186,187,188,193,194,195,196,199,200,201,202,257
The GROUP action with label N calculates somethingLi: 
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
=1-8:1,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256

The GROUP action with label Li calculates somethingene: 
ENERGY
Calculate the total potential energy of the simulation box. More details
The ENERGY action with label ene calculates somethingmax_H: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
 
SPECIESA
this keyword is used for colvars such as the coordination number
=H 
SPECIESB
this keyword is used for colvars such as the coordination number
=Li,N 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=1.6 D_MAX=5}  
MAX
calculate the maximum value
={BETA=0.05}

The COORDINATIONNUMBER action with label max_H calculates somethingghosta: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=0,0,20
The FIXEDATOM action with label ghosta calculates somethingNH3c: 
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
=257-260
The COM action with label NH3c calculates somethingdNH3hosta: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=ghosta,NH3c 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
The DISTANCE action with label dNH3hosta calculates the following quantities:
 Quantity   
 Description  
dNH3hosta.x
the x-component of the vector connecting the two atoms
dNH3hosta.y
the y-component of the vector connecting the two atoms
dNH3hosta.z
the z-component of the vector connecting the two atoms
dNH3hosta.value
the DISTANCE between this pair of atomsabs_dNH3hostaz: 
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 input to this function
=dNH3hosta.z 
FUNC
the function you wish to evaluate
=abs(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The MATHEVAL action with label abs_dNH3hostaz calculates somethinguwall1: 
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
=abs_dNH3hostaz 
AT
the positions of the wall
=11.0 
KAPPA
the force constant for the wall
=2000.0 
EXP
 the powers for the walls
=2 

The UPPER_WALLS action with label uwall1 calculates something
OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. More details
 ... 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=opes2
ARG
the input for this action is the scalar output from one or more other actions
=max_H.max 
PACE
the frequency for kernel deposition
=50
BARRIER
the free energy barrier to be overcome
=100 # #BIASFACTOR=20 # #KERNEL_CUTOFF=7.5 
TEMP
 temperature
=750
... OPES_METAD

The OPES_METAD action with label opes2 calculates the following quantities:
 Quantity   
 Description  
opes2.bias
the instantaneous value of the bias potential
opes2.rct
estimate of c(t)
opes2.zed
estimate of Z_n
opes2.neff
effective sample size
opes2.nker
total number of compressed kernels used to represent the bias
PRINT
Print quantities to a file. More details
 
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 
STRIDE
 the frequency with which the quantities of interest should be output
=2
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
=2