PLUMED-NEST

Project ID: plumID:22.008
Source: Ag6/T300/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
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A 
TIME
the units of time
=0.0101805 
ENERGY
the units of energy
=96.4853329
The UNITS action with label  calculates somethingcThe COORDINATION action with label c calculates the following quantities:
 Quantity   
 Type   
 Description  
c
scalar
the value of the coordination: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. More details
 
GROUPA
First list of atoms
=1-6 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=1-6 
R_0
The r_0 parameter of the switching function
=2.8
c: 
COORDINATION
Calculate coordination numbers. This action uses the defaults shown here. More details
 
GROUPA
First list of atoms
=1-6 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=1-6 
R_0
The r_0 parameter of the switching function
=2.8  
D_0
 The d_0 parameter of the switching function
=0.0 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=0
rThe GYRATION action with label r calculates the following quantities:
 Quantity   
 Type   
 Description  
r
scalar
the radius of gyration: 
GYRATION
Calculate the radius of gyration, or other properties related to it. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=1-6
rrotThe COMBINE action with label rrot calculates the following quantities:
 Quantity   
 Type   
 Description  
rrot
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=c,r 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.07534,0.99715 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
crotThe COMBINE action with label crot calculates the following quantities:
 Quantity   
 Type   
 Description  
crot
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=c,r 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.99715,-0.07534 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=rrot 
AT
the positions of the wall
=3.3 
KAPPA
the force constant for the wall
=50
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=crot 
AT
the positions of the wall
=8 
KAPPA
the force constant for the wall
=10
METAD
Used to performed metadynamics on one or more collective variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=crot,rrot 
SIGMA
the widths of the Gaussian hills
=0.3,0.03 
HEIGHT
the heights of the Gaussian hills
=0.2 
PACE
the frequency for hill addition
=100 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=50 
FILE
 a file in which the list of added hills is stored
=HILLS
FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=100