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=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
#RESTART
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A
The UNITS action with label  calculates somethingH: GROUPDefine 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 ATOMSthe 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: GROUPDefine 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 ATOMSthe 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: GROUPDefine 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 ATOMSthe 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: ENERGYCalculate the total potential energy of the simulation box. More details
The ENERGY action with label ene calculates somethingmax_nn_fix11: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=249 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=260 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.6 D_MAX=5}  MAXcalculate the maximum value={BETA=0.01}
The COORDINATIONNUMBER action with label max_nn_fix11 calculates the following quantities:
 Quantity   
 Description  
max_nn_fix11.max
the maximum colvar
max_nn_fix11.value
the coordination numbers of the specified atomsmax_nn_fix12: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=249 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=261 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.6 D_MAX=5}  MAXcalculate the maximum value={BETA=0.01}
The COORDINATIONNUMBER action with label max_nn_fix12 calculates the following quantities:
 Quantity   
 Description  
max_nn_fix12.max
the maximum colvar
max_nn_fix12.value
the coordination numbers of the specified atomsmax_nn_fix22: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=259 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=261 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.6 D_MAX=5}  MAXcalculate the maximum value={BETA=0.01}
The COORDINATIONNUMBER action with label max_nn_fix22 calculates the following quantities:
 Quantity   
 Description  
max_nn_fix22.max
the maximum colvar
max_nn_fix22.value
the coordination numbers of the specified atomsmax_nn_fix23: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=261 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=342 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.6 D_MAX=5}  MAXcalculate the maximum value={BETA=0.01}
The COORDINATIONNUMBER action with label max_nn_fix23 calculates the following quantities:
 Quantity   
 Description  
max_nn_fix23.max
the maximum colvar
max_nn_fix23.value
the coordination numbers of the specified atomsmax_nn_fix33: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=129 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=342 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.6 D_MAX=5}  MAXcalculate the maximum value={BETA=0.01}

The COORDINATIONNUMBER action with label max_nn_fix33 calculates the following quantities:
 Quantity   
 Description  
max_nn_fix33.max
the maximum colvar
max_nn_fix33.value
the coordination numbers of the specified atomsOPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. More details ... 
LABELa label for the action so that its output can be referenced in the input to other actions=opes2
ARGthe labels of the scalars on which the bias will act=max_nn_fix11.max # diazanediide anion was formed from  the first  layers  
PACEthe frequency for kernel deposition=250
BARRIERthe 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_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=Restart.data 
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=State_Bb220.data
STATE_WSTRIDEnumber 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 biasPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=80
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=400