PLUMED-NEST

Project ID: plumID:23.021
Source: plumed_metad/system1/1metad_DCM.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

ring: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=123-154 #heavy atoms dell'anello
c1: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=79,82,83,84,85 #anello sx
c2: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=38,39,37,12,13 #anello dx
p1: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=127,128,151,152,153,154
p2: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=142,143,147,148,149,150
p: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=p1,p2
The DISTANCE action with label p calculates a scalar quantityd1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=ring,c1
The DISTANCE action with label d1 calculates a scalar quantityd2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=ring,c2
The DISTANCE action with label d2 calculates a scalar quantityd: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=d1,d2 
FUNC
the function you wish to evaluate
=y-x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
 
ARG
the input for this action is the scalar output from one or more other actions
=d,p
 
HEIGHT
the heights of the Gaussian hills
=1
 
PACE
the frequency for hill addition
=500
 
SIGMA
the widths of the Gaussian hills
=0.1,0.05
 
GRID_MIN
the lower bounds for the grid
=-3,0
 
GRID_MAX
the upper bounds for the grid
=3,2
 
GRID_BIN
the number of bins for the grid
=200,200
 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=40
 
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

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
metad.rct
the reweighting factor $c(t)$
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d,p,metad 
FILE
the name of the file on which to output these quantities
=COLVAR 
STRIDE
 the frequency with which the quantities of interest should be output
=1000