PLUMED-NEST

Project ID: plumID:25.004
Source: NNH_form/700K/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 TIMEthe units of time=0.001  #Amstroeng, kJ/mol, fs

The UNITS action with label  calculates somethingHtot: 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=5,6,7,8,9,10,11,12,17,18,19,20,21,22,23,24,29,30,31,32,33,34,35,36,41,42,43,44,45,46,47,48,53,54,55,56,57,58,59,60,65,66,67,68,69,70,71,72,77,78,79,80,81,82,83,84,89,90,91,92,93,94,95,96,101,102,103,104,105,106,107,108,113,114,115,116,117,118,119,120,125,126,127,128,129,130,131,132,137,138,139,140,141,142,143,144,149,150,151,152,153,154,155,156,161,162,163,164,165,166,167,172,173,174,175,176,177,178,179,184,185,186,187,188,189,190,191,196,197,198,199,200,201,202,203,208,209,210,211,212,213,214,215,220,221,222,223,224,225,226,227,232,233,234,235,236,237,238,239,244,245,246,247,248,249,250,251,256,257,258,259,260,261,262,263,268,269,270,271,272,273,274,275,280,281,282,283,284,285,286,287,292,293,294,295,296,297,298,299,304,305,306,307,308,309,310,311,316,317,318,319,320,321,322,323,328,329,330,331,332,333,334,335,340,341,342,343,344,345,346,347,352,353,354,355,356,357,358,359,364,365,366,367,368,369,370,371,376,377,378,379,380,381,382,383,388,389,390,391,392,393,394,395,400,401,402,403,404,405,406,407,412,413,414,415,416,417,418,423,424,425,426,427,428,429,430,435,436,437,438,439,440,441,442,447,448,449,450,451,452,453,454,459,460,461,462,463,464,465,466,471,472,473,474,475,476,477,478,483,484,485,486,487,488,489,490,495,496,497,498,499,500,501,502,507,508,509,510,511,512,513,514,519,520,521,522,523,524,525,526,531,532,533,534,535,536,537,538,543,544,545,546,547,548,549,550,555,556,557,558,559,560,561,562,567,568,569,570,571,572,573,574,579,580,581,582,583,584,585,586,591,592,593,594,595,596,597,598,603,604,605,606,607,608,609,610,615,616,617,618,619,620,621,622,627,628,629,630,631,632,633,634,639,640,641,642,643,644,645,646,651,652,653,654,655,656,657,658,663,664,665,666,667,668,669,670,675,676,677,678,679,680,681,682,687,688,689,690,691,692,693,694,699,700,701,702,703,704,705,706,711,712,713,714,715,716,717,718,723,724,725,726,727,728,729,730,735,736,737,738,739,740,741,742,747,748,749,750,751,752,753,754
The GROUP action with label Htot 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=Htot REMOVEremove these atoms from the list=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,521,522,523,524,525,526,587,588,589,590,591,592,593,594,595,596,597,598,599,600,601,602,603,604,605,606,607,608,609,610,671,672,673,674,675,676,677,678,679,680,681,682,683,684,685,686,687,688,689,690,691,692,693,694
The GROUP action with label H calculates somethingBasup: 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=73,74,75,76,157,158,159,160,240,241,242,243,324,325,326,327,408,409,410,411,491,492,493,494,575,576,577,578,659,660,661,662,743,744,745,746
The GROUP action with label Basup calculates somethingN2: 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=755,756

The GROUP action with label N2 calculates somethingc: 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=N2 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=H R_0The r_0 parameter of the switching function=2.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12 MAXcalculate the maximum value={BETA=0.05}
The COORDINATIONNUMBER action with label c calculates the following quantities:
 Quantity   
 Description  
c.max
the maximum colvar
c.value
the coordination numbers of the specified atomsdNH: 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=N2 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=H MINcalculate the minimum value={BETA=20.0}
The DISTANCES action with label dNH calculates the following quantities:
 Quantity   
 Description  
dNH.min
the minimum colvar
dNH.value
the DISTANCES between the each pair of atoms that were specifieddNN: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPCalculate the distance between each distinct pair of atoms in the group=N2 MEAN calculate the mean of all the quantities

The DISTANCES action with label dNN calculates the following quantities:
 Quantity   
 Description  
dNN.mean
the mean of the colvars
dNN.value
the DISTANCES between the each pair of atoms that were specifieddz: 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=Basup GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=N2 MEAN calculate the mean of all the quantities

The ZDISTANCES action with label dz calculates the following quantities:
 Quantity   
 Description  
dz.mean
the mean of the colvars
dz.value
the DISTANCES between the each pair of atoms that were specifiedcHH: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=H R_0The r_0 parameter of the switching function=1.5 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12 MAXcalculate the maximum value={BETA=0.05}
The COORDINATIONNUMBER action with label cHH calculates the following quantities:
 Quantity   
 Description  
cHH.max
the maximum colvar
cHH.value
the coordination numbers of the specified atomsdHH: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPCalculate the distance between each distinct pair of atoms in the group=H MINcalculate the minimum value={BETA=20.0}
#uwall: UPPER_WALLS ARG=cHH.max AT=0.6 KAPPA=1000.0 EXP=2

The DISTANCES action with label dHH calculates the following quantities:
 Quantity   
 Description  
dHH.min
the minimum colvar
dHH.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=opes1
   ARGthe labels of the scalars on which the bias will act=dNH.min
   FILE a file in which the list of all deposited kernels is stored=Kernels1.data
   TEMP temperature=700
   PACEthe frequency for kernel deposition=500
   BARRIERthe free energy barrier to be overcome=70
   ADAPTIVE_SIGMA_STRIDEnumber of steps for measuring adaptive sigma=5001
   RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
   #EXCLUDED_REGION=target1
... OPES_METAD

The OPES_METAD action with label opes1 calculates the following quantities:
 Quantity   
 Description  
opes1.bias
the instantaneous value of the bias potential
opes1.rct
estimate of c(t)
opes1.zed
estimate of Z_n
opes1.neff
effective sample size
opes1.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=* STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR
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=1