PLUMED-NEST

Project ID: plumID:19.024
Source: INPUTS/plumed-pt-metad-wte.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

# Groups definition
h:    
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
=77,94,118,137,159,178,210,228
o:    
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
=92,116,135,157,169,183,219,250
core: 
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
=48,108,188,269

# CVs definition
s_a:  
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=h 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=o 
PAIR
 Pair only 1st element of the 1st group with 1st element in the second, etc
  
NN
 The n parameter of the switching function 
=8 
MM
 The m parameter of the switching function; 0 implies 2*NN
=12 
R_0
The r_0 parameter of the switching function
=0.25
The COORDINATION action with label s_a calculates a scalar quantitys_hc: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=core 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=core 
NN
 The n parameter of the switching function 
=8 
MM
 The m parameter of the switching function; 0 implies 2*NN
=12 
R_0
The r_0 parameter of the switching function
=0.50
The COORDINATION action with label s_hc calculates a scalar quantityene:  
ENERGY
Calculate the total potential energy of the simulation box. More details

# MetaD parameters
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
=s_a,s_hc 
SIGMA
the widths of the Gaussian hills
=0.4,0.4 
HEIGHT
the heights of the Gaussian hills
=2.5 
PACE
the frequency for hill addition
=250
  
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=8 
FILE
 a file in which the list of added hills is stored
=HILLS
... METAD

# WTE bias
The METAD action with label  calculates the following quantities:
 Quantity   
 Description  
.bias
the instantaneous value of the bias potential
EXTERNAL
Calculate a restraint that is defined on a grid that is read during start up More details
 
ARG
the input for this action is the scalar output from one or more other actions
=ene 
FILE
the name of the file containing the external potential
=BIAS