PLUMED-NEST-TEST-SITE

Project ID: plumID:21.015
Source: MetaD/CBM5/plumed.dat
Originally used with PLUMED version: 2.5
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

#RESTART
WHOLEMOLECULESThis 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=721-887

The WHOLEMOLECULES action with label  calculates somethinga1The CENTER_FAST action with label a1 calculates the following quantities:
 Quantity   
 Type   
 Description  
a1
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=798-801 
a2The CENTER_FAST action with label a2 calculates the following quantities:
 Quantity   
 Type   
 Description  
a2
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=803-807 
a3The CENTER_FAST action with label a3 calculates the following quantities:
 Quantity   
 Type   
 Description  
a3
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=832-835 
achiThe CENTER_FAST action with label achi calculates the following quantities:
 Quantity   
 Type   
 Description  
achi
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1-720 


p1The POSITION action with label p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
p1.x
scalar
the x-component of the atom position
p1.y
scalar
the y-component of the atom position
p1.z
scalar
the z-component of the atom position: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=a1 NOPBC ignore the periodic boundary conditions when calculating distances
p2The POSITION action with label p2 calculates the following quantities:
 Quantity   
 Type   
 Description  
p2.x
scalar
the x-component of the atom position
p2.y
scalar
the y-component of the atom position
p2.z
scalar
the z-component of the atom position: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=a2 NOPBC ignore the periodic boundary conditions when calculating distances
p3The POSITION action with label p3 calculates the following quantities:
 Quantity   
 Type   
 Description  
p3.x
scalar
the x-component of the atom position
p3.y
scalar
the y-component of the atom position
p3.z
scalar
the z-component of the atom position: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=a3 NOPBC ignore the periodic boundary conditions when calculating distances
pchiThe POSITION action with label pchi calculates the following quantities:
 Quantity   
 Type   
 Description  
pchi.x
scalar
the x-component of the atom position
pchi.y
scalar
the y-component of the atom position
pchi.z
scalar
the z-component of the atom position: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=achi NOPBC ignore the periodic boundary conditions when calculating distances


cThe COORDINATION action with label c calculates the following quantities:
 Quantity   
 Type   
 Description  
c
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=798-801,803-807,832-835 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=1-720 R_0The r_0 parameter of the switching function=0.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.7 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=100
c: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=798-801,803-807,832-835 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=1-720 R_0The r_0 parameter of the switching function=0.5 NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.7 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
distxThe MATHEVAL action with label distx calculates the following quantities:
 Quantity   
 Type   
 Description  
distx
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=p1.x,p2.x,p3.x,pchi.x VARthe names to give each of the arguments in the function=a,b,c,y FUNCthe function you wish to evaluate=((y-a)^2+(y-b)^2+(y-c)^2)^0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

METADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=c,distx
SIGMAthe widths of the Gaussian hills=0.5,0.5
HEIGHTthe heights of the Gaussian hills=2.0
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300
PACEthe frequency for hill addition=500
BIASFACTORuse well tempered metadynamics and use this bias factor=50.0
FILE a file in which the list of added hills is stored=HILLS
GRID_MINthe lower bounds for the grid=0.0,0.0
GRID_MAXthe upper bounds for the grid=75.0,35.0
GRID_BINthe number of bins for the grid=375,175
LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
... METAD

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=c,distx,metad.bias STRIDE the frequency with which the quantities of interest should be output=5000 FILEthe name of the file on which to output these quantities=COLVAR