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

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

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


The GROUP action with label Li calculates somethingene: ENERGYCalculate the total potential energy of the simulation box. More details
The ENERGY action with label ene calculates somethingmax_hh: 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=H 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=0.8 D_MAX=5 }  MAXcalculate the maximum value={BETA=0.05}
The COORDINATIONNUMBER action with label max_hh calculates the following quantities:
 Quantity   
 Description  
max_hh.max
the maximum colvar
max_hh.value
the coordination numbers of the specified atomsmax_hhg2: 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=388 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=0.8 D_MAX=5}  MAXcalculate the maximum value={BETA=0.05}

The COORDINATIONNUMBER action with label max_hhg2 calculates the following quantities:
 Quantity   
 Description  
max_hhg2.max
the maximum colvar
max_hhg2.value
the coordination numbers of the specified atomstarget: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=max_hhg2.max FUNCthe function you wish to evaluate=step(x-0.18) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The CUSTOM action with label target calculates the following quantities:
 Quantity   
 Description  
target.value
an arbitrary functionOPES_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_hhg2.max
PACEthe frequency for kernel deposition=500
BARRIERthe free energy barrier to be overcome=100 # #BIASFACTOR=20 # #KERNEL_CUTOFF=7.5
TEMP temperature=750
EXCLUDED_REGIONkernels 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_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_Bb100.data
STATE_WSTRIDEnumber 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 biasCOMMITTORDoes a committor analysis. More details ...
   ARGthe labels of the values which is being used to define the committor surface=max_hhg2.max
   STRIDE the frequency with which the CVs are analyzed=40
   BASIN_LL1List of lower limits for basin #=0.7
   BASIN_UL1List of upper limits for basin #=1.0
...

ghosta: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=0,0,15
The FIXEDATOM action with label ghosta calculates somethingdis_GH: ZDISTANCESCalculate the z components of the vectors connecting one or many pairs of atoms. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=ghosta GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=H MAXcalculate the maximum value={BETA=0.5}
The ZDISTANCES action with label dis_GH calculates the following quantities:
 Quantity   
 Description  
dis_GH.max
the maximum colvar
dis_GH.value
the DISTANCES between the each pair of atoms that were specifieduwall1: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dis_GH.max ATthe positions of the wall=12.0 KAPPAthe force constant for the wall=2000.0 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 potentialdis_GN: ZDISTANCESCalculate the z components of the vectors connecting one or many pairs of atoms. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=ghosta GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=N MAXcalculate the maximum value={BETA=0.5}
The ZDISTANCES action with label dis_GN calculates the following quantities:
 Quantity   
 Description  
dis_GN.max
the maximum colvar
dis_GN.value
the DISTANCES between the each pair of atoms that were specifieduwall2: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dis_GN.max ATthe positions of the wall=12.0 KAPPAthe force constant for the wall=2000.0 EXP the powers for the walls=2

The UPPER_WALLS action with label uwall2 calculates the following quantities:
 Quantity   
 Description  
uwall2.bias
the instantaneous value of the bias potential
uwall2.force2
the instantaneous value of the squared force due to this bias potentialmin_dishh: 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=388 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=H MINcalculate the minimum value={BETA=250}

The DISTANCES action with label min_dishh calculates the following quantities:
 Quantity   
 Description  
min_dishh.min
the minimum colvar
min_dishh.value
the DISTANCES between the each pair of atoms that were specifiedPRINTPrint 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=40
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