PLUMED-NEST

Project ID: plumID:22.006
Source: analysis/compute_weights.plumed
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.txt is generated by parse_atoms.py
# an example groups.txt file is included
INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
 
FILE
file to be included
=groups.txt
# The command:
# INCLUDE FILE=groups.txt
# ensures PLUMED loads the contents of the file called groups.txt
# The contents of this file are shown below (click the red comment to hide them).
c1: 
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
=5,6,7,9,20,21,22,24,40,41,42,44,60,61,62,64,70,71,72,74,80,81,82,84,95,99
c2: 
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
=104,105,106,108,119,120,121,123,139,140,141,143,159,160,161,163,169,170,171,173,179,180,181,183,194,198
c3: 
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
=203,204,205,207,225,226,227,229,245,246,247,249,265,266,267,269,275,276,277,279,285,286,287,289,307,311
c4: 
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
=316,317,318,320,338,339,340,342,358,359,360,362,378,379,380,382,388,389,390,392,398,399,400,402,420,424
# --- End of included input --- 
c1com: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=c1
c2com: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=c2
c3com: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=c3
c4com: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=c4

dist: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
GROUP
Calculate the distance between each distinct pair of atoms in the group
=c1com,c2com,c3com,c4com 
MEAN
 calculate the mean of all the quantities

rg1: 
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
=c1
rg2: 
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
=c2
rg3: 
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
=c3
rg4: 
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
=c4

rg: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=rg1,rg2,rg3,rg4 
NORMALIZE
 normalize all the coefficients so that in total they are equal to one
 
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
 ...
      
ARG
the input for this action is the scalar output from one or more other actions
=dist.mean,rg 
PACE
the frequency for hill addition
=100000000 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=5 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0 
SIGMA
the widths of the Gaussian hills
=0.05,0.01
      
GRID_MIN
the lower bounds for the grid
=0,0 
GRID_MAX
the upper bounds for the grid
=5,1.5  
GRID_BIN
the number of bins for the grid
=500,500 
HEIGHT
the heights of the Gaussian hills
=5
# Uncomment line when HILLS file is present      RESTART=YES FILE=HILLS
... METAD

The METAD action with label  calculates the following quantities:
 Quantity   
 Description  
.bias
the instantaneous value of the bias potentialbias: 
REWEIGHT_BIAS
Calculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More details
 
TEMP
the system temperature
=300.0
The REWEIGHT_BIAS action with label bias calculates a scalar quantity
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=2000 
FILE
the name of the file on which to output these quantities
=weights.dat 
ARG
the input for this action is the scalar output from one or more other actions
=bias