PLUMED-NEST

Project ID: plumID:20.007
Source: triple/plumed.dat
Originally used with PLUMED version: 2.4.2
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

# The commented out lines are the original implementation. They have been altered to be compatible with newer PLUMED versions.

d1775_2417: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1775,2417
The DISTANCE action with label d1775_2417 calculates a scalar quantityd1739_1755: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1739,1755
The DISTANCE action with label d1739_1755 calculates a scalar quantityd1795_453: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1795,453
The DISTANCE action with label d1795_453 calculates a scalar quantityd1809_1823: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1809,1823
The DISTANCE action with label d1809_1823 calculates a scalar quantityd1823_1834: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1823,1834

The DISTANCE action with label d1823_1834 calculates a scalar quantityloop_dist: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1772,1822
The DISTANCE action with label loop_dist calculates a scalar quantitypsi: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=1773,1775,1791,1793

The TORSION action with label psi calculates a scalar quantity
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rc1 
ARG
the input to this function
=d1775_2417,d1739_1755,d1795_453,d1809_1823,d1823_1834 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.41801464557647705,-0.04167945683002472,0.8776463866233826,-0.21770134568214417,0.07661298662424088 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... COMBINE

COMBINE
Calculate a polynomial combination of a set of other variables. More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rc2 
ARG
the input to this function
=d1775_2417,d1739_1755,d1795_453,d1809_1823,d1823_1834 
COEFFICIENTS
 the coefficients of the arguments in your function
=-0.7833237051963806,0.06509189307689667,0.42879876494407654,0.0804712250828743,-0.43797600269317627 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... COMBINE

METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
ARG
the input for this action is the scalar output from one or more other actions
=rc1,rc2
SIGMA
the widths of the Gaussian hills
=0.092,0.069
HEIGHT
the heights of the Gaussian hills
=1.5
PACE
the frequency for hill addition
=500
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
#GRID_MIN=0.0,-6.0
#GRID_MAX=8.0,2.0
#GRID_BIN=150,150
#REWEIGHTING_NGRID=150,150
... METAD

#PRINT ARG=d1775_2417,d1739_1755,d1795_453,d1809_1823,d1823_1834,loop_dist,psi,rc1,rc2,metad.bias,metad.rbias STRIDE=1 FILE=BIASED_COLVAR

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1775_2417,d1739_1755,d1795_453,d1809_1823,d1823_1834,loop_dist,psi,rc1,rc2,metad.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=1 
FILE
the name of the file on which to output these quantities
=BIASED_COLVAR