PLUMED-NEST

Project ID: plumID:23.028
Source: DeepMD_simulations/Kinetic_rate/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
=27,28,29,30,31,32,33,34,35,36,54,55,56,57,58,59,62,86,87,88,89,90,91,92,93,94,136,137,138,139,140,141,142,143,144,145,146,147,148,164,165,166,167,168,183,184,185,186,187,209,210,211,221,222,223,227,261,262,263,264,265,266,267,268,269,270,271,272,273,274,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,375,376,377,378,379,382,384,385,386,388,389,390

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
=17,18,19,20,21,22,23,24,25,26,48,49,50,51,52,53,61,77,78,79,80,81,82,83,84,85,123,124,125,126,127,128,129,130,131,132,133,134,135,159,160,161,162,163,178,179,180,181,182,206,207,208,218,219,220,226,247,248,249,250,251,252,253,254,255,256,257,258,259,260,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,370,371,372,373,374,381,383,387

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
=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,37,38,39,40,41,42,43,44,45,46,47,60,63,64,65,66,67,68,69,70,71,72,73,74,75,76,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,149,150,151,152,153,154,155,156,157,158,169,170,171,172,173,174,175,176,177,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,212,213,214,215,216,217,224,225,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,360,361,362,363,364,365,366,367,368,369,380


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_hh: 
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
=H 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=0.8 D_MAX=5 }  
MAX
calculate the maximum value
={BETA=0.05}
The COORDINATIONNUMBER action with label max_hh calculates somethingmax_hhg2: 
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
=388 
SPECIESB
this keyword is used for colvars such as the coordination number
=H 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=0.8 D_MAX=5}  
MAX
calculate the maximum value
={BETA=0.05}

The COORDINATIONNUMBER action with label max_hhg2 calculates somethingtarget: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=max_hhg2.max 
FUNC
the function you wish to evaluate
=step(x-0.18 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The CUSTOM action with label target 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_hhg2.max
PACE
the frequency for kernel deposition
=500
BARRIER
the free energy barrier to be overcome
=100 # #BIASFACTOR=20 # #KERNEL_CUTOFF=7.5
TEMP
 temperature
=750
EXCLUDED_REGION
kernels are not deposited when the action provided here has a nonzero value, see example above
=target
#RESTART=NO
FILE
 a file in which the list of all deposited kernels is stored
=Kernels_Bb100.data.data
STATE_RFILE
read from this file the compressed kernels and all the info needed to RESTART the simulation
=Restart.data
STATE_WFILE
write to this file the compressed kernels and all the info needed to RESTART the simulation
=State_Bb100.data
STATE_WSTRIDE
number of MD steps between writing the STATE_WFILE
=500
STORE_STATES
 append to STATE_WFILE instead of ovewriting it each time
... 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
COMMITTOR
Does a committor analysis. More details
 ...
   
ARG
the input for this action is the scalar output from one or more other actions
=max_hhg2.max
   
STRIDE
 the frequency with which the CVs are analyzed
=40
   
BASIN_LL1
List of lower limits for basin #
=0.7
   
BASIN_UL1
List of upper limits for basin #
=1.0
...

ghosta: 
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=0,0,15
The FIXEDATOM action with label ghosta calculates somethingdis_GH: 
ZDISTANCES
Calculate the z components of the vectors connecting one or many pairs of atoms. More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=ghosta 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=H 
MAX
calculate the maximum value
={BETA=0.5}
The ZDISTANCES action with label dis_GH 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
=dis_GH.max 
AT
the positions of the wall
=12.0 
KAPPA
the force constant for the wall
=2000.0 
EXP
 the powers for the walls
=2
The UPPER_WALLS action with label uwall1 calculates somethingdis_GN: 
ZDISTANCES
Calculate the z components of the vectors connecting one or many pairs of atoms. More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=ghosta 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=N 
MAX
calculate the maximum value
={BETA=0.5}
The ZDISTANCES action with label dis_GN calculates somethinguwall2: 
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
=dis_GN.max 
AT
the positions of the wall
=12.0 
KAPPA
the force constant for the wall
=2000.0 
EXP
 the powers for the walls
=2

The UPPER_WALLS action with label uwall2 calculates somethingmin_dishh: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=388 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=H 
MIN
calculate the minimum value
={BETA=250}

The DISTANCES action with label min_dishh calculates something
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
=40
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
=400