PLUMED-NEST

Project ID: plumID:23.028
Source: DeepMD_simulations/Biased/plumed_min_n1h.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=27,28,29,30,31,32,33,34,35,36,54,55,56,57,58,59,62,86,87,88,89,90,91,92,93,94,136,137,138,139,140,141,142,143,144,145,146,147,148,164,165,166,167,168,183,184,185,186,187,209,210,211,221,222,223,227,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,377,378,379,380,381,384,386,387,388,390,391,392,394

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=17,18,19,20,21,22,23,24,25,26,48,49,50,51,52,53,61,77,78,79,80,81,82,83,84,85,123,124,125,126,127,128,129,130,131,132,133,134,135,159,160,161,162,163,178,179,180,181,182,206,207,208,218,219,220,226,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,372,373,374,375,376,383,385,389,393

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 somethingSGN: 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=84,85

The GROUP action with label SGN calculates somethingene: ENERGYCalculate the total potential energy of the simulation box. More details
The ENERGY action with label ene calculates somethingmax_nn: 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=N SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=N 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 calculates the following quantities:
 Quantity   
 Description  
max_nn.max
the maximum colvar
max_nn.value
the coordination numbers of the specified atomsmin_GNH: 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=SGN SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=H 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=1.5 D_MAX=5}  MINcalculate the minimum value={BETA=2}
The COORDINATIONNUMBER action with label min_GNH calculates the following quantities:
 Quantity   
 Description  
min_GNH.min
the minimum colvar
min_GNH.value
the coordination numbers of the specified atomsdis_GNH: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=SGN GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=H LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.6 NN=8 MM=16}

The DISTANCES action with label dis_GNH calculates the following quantities:
 Quantity   
 Description  
dis_GNH.lessthan
the number of colvars that have a value less than a threshold
dis_GNH.value
the DISTANCES between the each pair of atoms that were specifiedOPES_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=min_GNH.min
PACEthe frequency for kernel deposition=250
BARRIERthe free energy barrier to be overcome=60
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 biaslwall1: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=max_nn.max ATthe positions of the wall=0.4 KAPPAthe force constant for the wall=1000.0 EXP the powers for the walls=2
The LOWER_WALLS action with label lwall1 calculates the following quantities:
 Quantity   
 Description  
lwall1.bias
the instantaneous value of the bias potential
lwall1.force2
the instantaneous value of the squared force due to this bias potentialuwall1: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dis_GNH.lessthan ATthe positions of the wall=3.0 KAPPAthe force constant for the wall=1000.0 EXP the powers for the walls=2

The UPPER_WALLS action with label uwall1 calculates the following quantities:
 Quantity   
 Description  
uwall1.bias
the instantaneous value of the bias potential
uwall1.force2
the instantaneous value of the squared force due to this bias potentialPRINTPrint 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=60
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