PLUMED-NEST-TEST-SITE

Project ID: plumID:23.021
Source: plumed_metad/system3/metad_syst3.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

ringThe CENTER_FAST action with label ring calculates the following quantities:
 Quantity   
 Type   
 Description  
ring
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=515-614
c1The CENTER_FAST action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
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=1-60 #fullerene cx
c2The CENTER_FAST action with label c2 calculates the following quantities:
 Quantity   
 Type   
 Description  
c2
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=123-182 #fullerene sx
c3The CENTER_FAST action with label c3 calculates the following quantities:
 Quantity   
 Type   
 Description  
c3
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=343-402 #fullerene dx
d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
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=ring,c2
d2The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
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=ring,c3
dThe CUSTOM action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1,d2 FUNCthe function you wish to evaluate=y-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
#restrain stoppers to keep distance from center
aThe FIXEDATOM action with label a calculates the following quantities:
 Quantity   
 Type   
 Description  
a
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.822783,3.843150,-3.996667
a: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=2.822783,3.843150,-3.996667  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
bThe FIXEDATOM action with label b calculates the following quantities:
 Quantity   
 Type   
 Description  
b
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=-2.826600,3.851033,3.999600
b: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=-2.826600,3.851033,3.999600  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
r1The DISTANCE action with label r1 calculates the following quantities:
 Quantity   
 Type   
 Description  
r1
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=c2,a
r2The DISTANCE action with label r2 calculates the following quantities:
 Quantity   
 Type   
 Description  
r2
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=c3,b
wThe UPPER_WALLS action with label w calculates the following quantities:
 Quantity   
 Type   
 Description  
w.bias
scalar
the instantaneous value of the bias potential
w.force2
scalar
the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=1,1 ARGthe arguments on which the bias is acting=r1,r2 KAPPAthe force constant for the wall=200,200
METADUsed to performed metadynamics on one or more collective variables. More details ...
 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.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
metad.rct
scalar
the reweighting factor c(t).
 ARGthe labels of the scalars on which the bias will act=d
 HEIGHTthe heights of the Gaussian hills=1
 PACEthe frequency for hill addition=500
 SIGMAthe widths of the Gaussian hills=0.1
 GRID_MINthe lower bounds for the grid=-6
 GRID_MAXthe upper bounds for the grid=6
 GRID_BINthe number of bins for the grid=200
 BIASFACTORuse well tempered metadynamics and use this bias factor=25
 FILE a file in which the list of added hills is stored=HILLS
 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... METAD
potentialThe MATHEVAL action with label potential calculates the following quantities:
 Quantity   
 Type   
 Description  
potential
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=metad.bias,w.bias FUNCthe function you wish to evaluate=x+y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO 
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d,metad.*,potential,w.bias FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=1000