PLUMED-NEST

Project ID: plumID:25.004
Source: NH3_formation/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 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 somethingHr: 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=759,760

The GROUP action with label Hr 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=Hr 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=Hr 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 specifieddNH1: 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=756 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=Hr MINcalculate the minimum value={BETA=20.0} MAXcalculate the maximum value={BETA=0.05}

The DISTANCES action with label dNH1 calculates the following quantities:
 Quantity   
 Description  
dNH1.min
the minimum colvar
dNH1.max
the maximum colvar
dNH1.value
the DISTANCES between the each pair of atoms that were specifieddHH: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPCalculate the distance between each distinct pair of atoms in the group=Hr 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 specifieduwall1: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dNH1.max ATthe positions of the wall=5.0 KAPPAthe force constant for the wall=200 EXP the powers for the walls=2.0

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 potentialtarget1: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dNH.min FUNCthe function you wish to evaluate=step(2-x) 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=dNH1.min
   FILE a file in which the list of all deposited kernels is stored=Kernels1.data
   TEMP temperature=550
   PACEthe frequency for kernel deposition=200
   BARRIERthe free energy barrier to be overcome=40
   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=dNH1.min
  STRIDE the frequency with which the CVs are analyzed=5000
  BASIN_LL1List of lower limits for basin #=0.0
  BASIN_UL1List of upper limits for basin #=1.1
... 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