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: 
GROUP
Define 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
 
ATOMS
the 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: 
GROUP
Define 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
 
ATOMS
the 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: 
GROUP
Define 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
 
ATOMS
the 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: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the 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: 
GYRATION
Calculate 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 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=cas
ENERGY
Calculate the total potential energy of the simulation box. More details
 
LABEL
a 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 value calculated by this action

#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: 
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 ...
    
ARG
the arguments on which the bias is acting
=dend
    
AT
the 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:

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=dend,en,p.bias,p.force2 
STRIDE
 the frequency with which the quantities of interest should be output
=1000 
FILE
the name of the file on which to output these quantities
=helix_sf_f-4.5_eps7.5_10000000.en.colvars.dat 
FMT
the format that should be used to output real numbers
=%8.4f