PLUMED-NEST

Click on the labels of the actions for more information on what each action computes

gA: 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=1-256
The GROUP action with label gA calculates somethinggB: 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=938-1660

The GROUP action with label gB calculates somethingcomA: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=gA
The COM action with label comA calculates somethingcomB: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=gB

The COM action with label comB calculates somethingd: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=comA,comB

The DISTANCE action with label d calculates the following quantities:
 Quantity   
 Description  
d.value
the DISTANCE between this pair of atomsuw: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d ATthe positions of the wall=7.3 KAPPAthe force constant for the wall=10000

The UPPER_WALLS action with label uw calculates the following quantities:
 Quantity   
 Description  
uw.bias
the instantaneous value of the bias potential
uw.force2
the instantaneous value of the squared force due to this bias potentialmetad: METADUsed to performed metadynamics on one or more collective variables. More details ...
  ARGthe labels of the scalars on which the bias will act=d
  SIGMAthe widths of the Gaussian hills=0.005
  #HEIGHT=0.04184 
  HEIGHTthe heights of the Gaussian hills=0.4184 
  PACEthe frequency for hill addition=45
  FILE a file in which the list of added hills is stored=HILLS
...


The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialPRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR