PLUMED-NEST

Project ID: plumID:23.028
Source: DeepMD_simulations/FES_calculation/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
=27,28,29,30,31,32,33,34,35,36,54,55,56,57,58,59,62,86,87,88,89,90,91,92,93,94,136,137,138,139,140,141,142,143,144,145,146,147,148,164,165,166,167,168,183,184,185,186,187,209,210,211,221,222,223,227,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,377,378,379,380,381,384,386,387,388,390,391,392

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
=17,18,19,20,21,22,23,24,25,26,48,49,50,51,52,53,61,77,78,79,80,81,82,83,84,85,123,124,125,126,127,128,129,130,131,132,133,134,135,159,160,161,162,163,178,179,180,181,182,206,207,208,218,219,220,226,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,372,373,374,375,376,383,385,389

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
=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,37,38,39,40,41,42,43,44,45,46,47,60,63,64,65,66,67,68,69,70,71,72,73,74,75,76,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,149,150,151,152,153,154,155,156,157,158,169,170,171,172,173,174,175,176,177,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,212,213,214,215,216,217,224,225,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,362,363,364,365,366,367,368,369,370,371,382

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_nn_fix11: 
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
=249 
SPECIESB
this keyword is used for colvars such as the coordination number
=260 
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=0.01}
The COORDINATIONNUMBER action with label max_nn_fix11 calculates somethingmax_nn_fix12: 
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
=249 
SPECIESB
this keyword is used for colvars such as the coordination number
=261 
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=0.01}
The COORDINATIONNUMBER action with label max_nn_fix12 calculates somethingmax_nn_fix22: 
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
=259 
SPECIESB
this keyword is used for colvars such as the coordination number
=261 
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=0.01}
The COORDINATIONNUMBER action with label max_nn_fix22 calculates somethingmax_nn_fix23: 
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
=261 
SPECIESB
this keyword is used for colvars such as the coordination number
=342 
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=0.01}
The COORDINATIONNUMBER action with label max_nn_fix23 calculates somethingmax_nn_fix33: 
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
=129 
SPECIESB
this keyword is used for colvars such as the coordination number
=342 
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=0.01}

The COORDINATIONNUMBER action with label max_nn_fix33 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_nn_fix11.max # diazanediide anion was formed from  the first  layers  
PACE
the frequency for kernel deposition
=250
BARRIER
the free energy barrier to be overcome
=220 
TEMP
 temperature
=750
#RESTART=NO
FILE
 a file in which the list of all deposited kernels is stored
=Kernels_Bb220.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_Bb220.data
STATE_WSTRIDE
number of MD steps between writing the STATE_WFILE
=2000
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
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
=80
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