PLUMED-NEST-TEST-SITE

Project ID: plumID:21.015
Source: US/CBM5/plumed9.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

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

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

restraint-bndThe RESTRAINT action with label restraint-bnd calculates the following quantities:
 Quantity   
 Type   
 Description  
restraint-bnd.bias
scalar
the instantaneous value of the bias potential
restraint-bnd.force2
scalar
the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=distx KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100.0 ATthe position of the restraint=2.6
restraint-bnd: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=distx KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100.0 ATthe position of the restraint=2.6  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=distx,restraint-bnd.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=COLVAR9