PLUMED-NEST-TEST-SITE

Project ID: plumID:25.004
Source: H2_flooding/coverage_16.7/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=25,26,27,28,37,38,39,40,49,50,51,52,61,62,63,64,72,73,74,75,108,109,110,111,119,120,121,122,131,132,133,134,143,144,145,146,155,156,157,158,191,192,193,194,203,204,205,206,215,216,217,218,227,228,229,230,239,240,241,242,274,275,276,277,286,287,288,289,298,299,300,301,310,311,312,313,321,322,323,324,357,358,359,360,369,370,371,372,381,382,383,384,393,394,395,396,405,406,407,408,441,442,443,453,454,455,456,465,466,467,468,477,478,479,480,489,490,491,492,525,526,527,528,537,538,539,540,549,550,551,552,561,562,563,564,573,574,575,576,609,610,611,612,621,622,623,624,633,634,635,636,645,646,647,648,657,658,659,660,693,694,695,696,705,706,707,708,717,718,719,720,728,729,730,731,740,741,742,743
# Remove H of NH.
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=751,752,753,754,755,756
REMOVEremove these atoms from the list=5,6,7,8,9,10,11,12,17,18,19,20,21,22,23,24,88,89,90,91,92,93,94,95,100,101,102,103,104,105,106,107,171,172,173,174,175,176,177,178,183,184,185,186,187,188,189,190,254,255,256,257,258,259,260,261,266,267,268,269,270,271,272,273,337,338,339,340,341,342,343,344,349,350,351,352,353,354,355,356,421,422,423,424,425,426,427,428,433,434,435,436,437,438,439,440,505,506,507,508,509,510,511,512,517,518,519,520,521,522,523,524,589,590,591,592,593,594,595,596,601,602,603,604,605,606,607,608,673,674,675,676,677,678,679,680,685,686,687,688,689,690,691,692,755,753,751,754,750,756

The GROUP action with label H calculates somethinga: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=0,0,47.5

The FIXEDATOM action with label a calculates somethingdHH: 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}
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 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 atomsdz: 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=a GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=H MAXcalculate the maximum value={BETA=0.05}

The ZDISTANCES action with label dz calculates the following quantities:
 Quantity   
 Description  
dz.max
the maximum colvar
dz.value
the DISTANCES between the each pair of atoms that were specifiedtarget1: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cHH.max FUNCthe function you wish to evaluate=step(x-0.8) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

The CUSTOM action with label target1 calculates the following quantities:
 Quantity   
 Description  
target1.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=opes1
   ARGthe labels of the scalars on which the bias will act=cHH.max
   FILE a file in which the list of all deposited kernels is stored=Kernels1.data
   TEMP temperature=700
   PACEthe frequency for kernel deposition=250
   BARRIERthe free energy barrier to be overcome=60
   #ADAPTIVE_SIGMA_STRIDE=5001
   RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
   EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=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 biasCOMMITTORDoes a committor analysis. More details ...
   ARGthe labels of the values which is being used to define the committor surface=dz.max
   STRIDE the frequency with which the CVs are analyzed=1000
   BASIN_LL1List of lower limits for basin #=6.0
   BASIN_UL1List of upper limits for basin #=15.0
   FILEthe name of the file on which to output the reached basin=FORMATION
... COMMITTOR

PRINTPrint 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=10 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