PLUMED-NEST

Project ID: plumID:24.035
Source: notebooks/1_exploration/N2_flooding_inputs/plumed-fresh.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

# Template file for PLUMED: Opes-flooding for N2 / FeCo

#RESTART

UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A

### GROUPS

The UNITS action with label  calculates somethingN1The GROUP action with label N1 calculates the following quantities:
 Quantity   
 Type   
 Description  
N1
atoms
indices of atoms specified in GROUP:   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=121
N2The GROUP action with label N2 calculates the following quantities:
 Quantity   
 Type   
 Description  
N2
atoms
indices of atoms specified in GROUP:   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=122
NThe GROUP action with label N calculates the following quantities:
 Quantity   
 Type   
 Description  
N
atoms
indices of atoms specified in GROUP:    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=121,122
FeThe GROUP action with label Fe calculates the following quantities:
 Quantity   
 Type   
 Description  
Fe
atoms
indices of atoms specified in GROUP:   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=1,3,5,7,9,11,13,15,17,19,21,23,25,27,29,31,33,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,79,81,83,85,87,89,91,93,95,97,99,101,103,105,107,109,111,113,115,117,119
CoThe GROUP action with label Co calculates the following quantities:
 Quantity   
 Type   
 Description  
Co
atoms
indices of atoms specified in GROUP:   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=2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,58,60,62,64,66,68,70,72,74,76,78,80,82,84,86,88,90,92,94,96,98,100,102,104,106,108,110,112,114,116,118,120
FeCoThe GROUP action with label FeCo calculates the following quantities:
 Quantity   
 Type   
 Description  
FeCo
atoms
indices of atoms specified in GROUP: 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=1,3,5,7,9,11,13,15,17,19,21,23,25,27,29,31,33,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,79,81,83,85,87,89,91,93,95,97,99,101,103,105,107,109,111,113,115,117,119,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,58,60,62,64,66,68,70,72,74,76,78,80,82,84,86,88,90,92,94,96,98,100,102,104,106,108,110,112,114,116,118,120

### COLLECTIVE VARIABLES

# Coordination Numbers
coord_N-FeThe COORDINATION action with label coord_N-Fe calculates the following quantities:
 Quantity   
 Type   
 Description  
coord_N-Fe
scalar
the value of the coordination:   COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=N GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=Fe   D_0 The d_0 parameter of the switching function=1.0 R_0The r_0 parameter of the switching function=1.5
coord_N-Fe:   COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=N GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=Fe   D_0 The d_0 parameter of the switching function=1.0 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=0
coord_N-CoThe COORDINATION action with label coord_N-Co calculates the following quantities:
 Quantity   
 Type   
 Description  
coord_N-Co
scalar
the value of the coordination:   COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=N GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=Co   D_0 The d_0 parameter of the switching function=1.0 R_0The r_0 parameter of the switching function=1.5
coord_N-Co:   COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=N GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=Co   D_0 The d_0 parameter of the switching function=1.0 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=0
coord_N-FeCoThe COORDINATION action with label coord_N-FeCo calculates the following quantities:
 Quantity   
 Type   
 Description  
coord_N-FeCo
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=N GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=FeCo D_0 The d_0 parameter of the switching function=1.0 R_0The r_0 parameter of the switching function=1.5
coord_N-FeCo: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=N GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=FeCo D_0 The d_0 parameter of the switching function=1.0 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=0

# Distance between N-N
d_N-NThe DISTANCE action with label d_N-N calculates the following quantities:
 Quantity   
 Type   
 Description  
d_N-N
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=N1,N2

# Define excluded_region
excludeThe CUSTOM action with label exclude calculates the following quantities:
 Quantity   
 Type   
 Description  
exclude
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d_N-N FUNCthe function you wish to evaluate=step(x-1.5) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

### BIAS 

# Opes 
biasThe OPES_METAD action with label bias calculates the following quantities:
 Quantity   
 Type   
 Description  
bias.bias
scalar
the instantaneous value of the bias potential
bias.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
bias.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
bias.neff
scalar
effective sample size
bias.nker
scalar
total number of compressed kernels used to represent the bias: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=d_N-N,coord_N-Fe BARRIERthe free energy barrier to be overcome=50 TEMP temperature=700 PACEthe frequency for kernel deposition=50 EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=exclude RESTARTallows per-action setting of restart (YES/NO/AUTO)=YES
bias: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=d_N-N,coord_N-Fe BARRIERthe free energy barrier to be overcome=50 TEMP temperature=700 PACEthe frequency for kernel deposition=50 EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=exclude RESTARTallows per-action setting of restart (YES/NO/AUTO)=YES  SIGMA the initial widths of the kernels=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1 FILE a file in which the list of all deposited kernels is stored=KERNELS

# Harmonic lower wall to prevent N2 desorption 
lwallThe LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall.bias
scalar
the instantaneous value of the bias potential
lwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=coord_N-Fe ATthe positions of the wall=0.2 KAPPAthe force constant for the wall=10000. EXP the powers for the walls=2

### STOP the simulation when the system reaches the products state
COMMITTORDoes a committor analysis. More details ARGthe labels of the values which is being used to define the committor surface=d_N-N STRIDE the frequency with which the CVs are analyzed=1 BASIN_LL1List of lower limits for basin #=2.5 BASIN_UL1List of upper limits for basin #=10 

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=100 FILEthe name of the file on which to output these quantities=COLVAR