PLUMED-NEST

Project ID: plumID:21.032
Source: plumed_PB_WTMetad.dat
Originally used with PLUMED version: 2.6
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

UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A ENERGYthe units of energy=kcal/mol 
The UNITS action with label  calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-774 STRIDE the frequency with which molecules are reassembled=1


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=67,88,243,292 LABELa label for the action so that its output can be referenced in the input to other actions=comCysZn69The GROUP action with label comCysZn69 calculates the following quantities:
 Quantity   
 Type   
 Description  
comCysZn69
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=152,88,324,173 LABELa label for the action so that its output can be referenced in the input to other actions=comCysZn68The GROUP action with label comCysZn68 calculates the following quantities:
 Quantity   
 Type   
 Description  
comCysZn68
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=211,292,359,173 LABELa label for the action so that its output can be referenced in the input to other actions=comCysZn67The GROUP action with label comCysZn67 calculates the following quantities:
 Quantity   
 Type   
 Description  
comCysZn67
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=465,455,628,434 LABELa label for the action so that its output can be referenced in the input to other actions=comCysZn66The GROUP action with label comCysZn66 calculates the following quantities:
 Quantity   
 Type   
 Description  
comCysZn66
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=512,554,465,761 LABELa label for the action so that its output can be referenced in the input to other actions=comCysZn65The GROUP action with label comCysZn65 calculates the following quantities:
 Quantity   
 Type   
 Description  
comCysZn65
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=599,424,434,554 LABELa label for the action so that its output can be referenced in the input to other actions=comCysZn64The GROUP action with label comCysZn64 calculates the following quantities:
 Quantity   
 Type   
 Description  
comCysZn64
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=751,761,730,628 LABELa label for the action so that its output can be referenced in the input to other actions=comCysZn63The GROUP action with label comCysZn63 calculates the following quantities:
 Quantity   
 Type   
 Description  
comCysZn63
atoms
indices of atoms specified in GROUP



zn69The COORDINATION action with label zn69 calculates the following quantities:
 Quantity   
 Type   
 Description  
zn69
scalar
the value of the coordination:  COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=781 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=comCysZn69 R_0The r_0 parameter of the switching function=3.5  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100
zn69:  COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=781 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=comCysZn69 R_0The r_0 parameter of the switching function=3.5  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100  D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
zn68The COORDINATION action with label zn68 calculates the following quantities:
 Quantity   
 Type   
 Description  
zn68
scalar
the value of the coordination:  COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=780 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=comCysZn68 R_0The r_0 parameter of the switching function=3.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100 
zn68:  COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=780 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=comCysZn68 R_0The r_0 parameter of the switching function=3.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100  D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
zn67The COORDINATION action with label zn67 calculates the following quantities:
 Quantity   
 Type   
 Description  
zn67
scalar
the value of the coordination:  COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=779 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=comCysZn67 R_0The r_0 parameter of the switching function=3.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100 
zn67:  COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=779 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=comCysZn67 R_0The r_0 parameter of the switching function=3.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100  D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
zn66The COORDINATION action with label zn66 calculates the following quantities:
 Quantity   
 Type   
 Description  
zn66
scalar
the value of the coordination:  COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=778  GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=comCysZn66 R_0The r_0 parameter of the switching function=3.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100 
zn66:  COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=778  GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=comCysZn66 R_0The r_0 parameter of the switching function=3.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100  D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
zn65The COORDINATION action with label zn65 calculates the following quantities:
 Quantity   
 Type   
 Description  
zn65
scalar
the value of the coordination:  COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=777 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=comCysZn65 R_0The r_0 parameter of the switching function=3.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100 
zn65:  COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=777 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=comCysZn65 R_0The r_0 parameter of the switching function=3.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100  D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
zn64The COORDINATION action with label zn64 calculates the following quantities:
 Quantity   
 Type   
 Description  
zn64
scalar
the value of the coordination:  COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=776 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=comCysZn64 R_0The r_0 parameter of the switching function=3.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100 
zn64:  COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=776 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=comCysZn64 R_0The r_0 parameter of the switching function=3.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100  D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
zn63The COORDINATION action with label zn63 calculates the following quantities:
 Quantity   
 Type   
 Description  
zn63
scalar
the value of the coordination:  COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=775  GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=comCysZn63 R_0The r_0 parameter of the switching function=3.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100  
zn63:  COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=775  GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=comCysZn63 R_0The r_0 parameter of the switching function=3.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100  D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0


PBMETADUsed to performed Parallel Bias metadynamics. More details ...
ARGthe labels of the scalars on which the bias will act=zn69,zn68,zn67,zn66,zn65,zn64,zn63
PACEthe frequency for hill addition, one for all biases=500 BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=18.0 HEIGHTthe height of the Gaussian hills, one for all biases=0.6 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0
INTERVAL_MINone dimensional lower limits, outside the limits the system will not feel the biasing force=0.4,0.4,0.4,0.4,0.4,0.4,0.4
INTERVAL_MAXone dimensional upper limits, outside the limits the system will not feel the biasing force=4,4,4,4,4,4,4
SIGMAthe widths of the Gaussian hills=0.15,0.15,0.15,0.15,0.15,0.15,0.15
GRID_MINthe lower bounds for the grid=0,0,0,0,0,0,0
GRID_MAXthe upper bounds for the grid=30,30,30,30,30,30,30
WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
FILEfiles in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found=HILLS_69,HILLS_68,HILLS_67,HILLS_66,HILLS_65,HILLS_64,HILLS_63 LABELa label for the action so that its output can be referenced in the input to other actions=metadThe PBMETAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
... PBMETAD