PLUMED-NEST

Project ID: plumID:20.017
Source: beaded-helix/helix_sf_f-4.5_eps7.5_10000000.plumed.dat
Originally used with PLUMED version: 2.7
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

#UNITS LENGTH=A TIME=fs ENERGY=kcal/mol

b1The GROUP action with label b1 calculates the following quantities:
 Quantity   
 Type   
 Description  
b1
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=1
b2The GROUP action with label b2 calculates the following quantities:
 Quantity   
 Type   
 Description  
b2
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=12
casThe GROUP action with label cas calculates the following quantities:
 Quantity   
 Type   
 Description  
cas
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=1-12

dendThe DISTANCE action with label dend calculates the following quantities:
 Quantity   
 Type   
 Description  
dend
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=b1,b2
rgThe GYRATION action with label rg calculates the following quantities:
 Quantity   
 Type   
 Description  
rg
scalar
the radius of gyration: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=cas
ENERGYCalculate the total potential energy of the simulation box. More details LABELa label for the action so that its output can be referenced in the input to other actions=enThe ENERGY action with label en calculates the following quantities:
 Quantity   
 Type   
 Description  
en
scalar
the internal energy

#The conversion factor is 69.4786 pN = 1 kcal/mol/Angstrom
#100pN = 1.4425 kcal/mol/A
pThe RESTRAINT action with label p calculates the following quantities:
 Quantity   
 Type   
 Description  
p.bias
scalar
the instantaneous value of the bias potential
p.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. More details ...
    ARGthe values the harmonic restraint acts upon=dend
    ATthe position of the restraint=0
    SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=-4.5
    KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=0
... p:

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=dend,en,p.bias,p.force2 STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=helix_sf_f-4.5_eps7.5_10000000.en.colvars.dat FMTthe format that should be used to output real numbers=%8.4f