PLUMED-NEST

Project ID: plumID:21.021
Source: meta_inputs/tetrapept_2D/plumed_biased.dat
Originally used with PLUMED version: 2.7-mod
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

t1: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=5,7,9,15
The TORSION action with label t1 calculates a scalar quantityt2: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=7,9,15,17
The TORSION action with label t2 calculates a scalar quantityt3: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=15,17,19,25
The TORSION action with label t3 calculates a scalar quantityt4: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=17,19,25,27
The TORSION action with label t4 calculates a scalar quantityt5: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=25,27,29,35
The TORSION action with label t5 calculates a scalar quantityt6: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=27,29,35,37

The TORSION action with label t6 calculates a scalar quantity
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-42
gyr: 
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
=5,15,25,35,9,19,29,11,21,31,2,39,7,17,27,37,6,16,26,36

hy: 
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
=8,18,28,38
ox: 
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
=6,16,26,36
c1: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=ox 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=hy  
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={CUBIC D_0=3 D_MAX=4}

The COORDINATION action with label c1 calculates a scalar quantitymt: 
METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
PACE
the frequency for hill addition
=500
ARG
the input for this action is the scalar output from one or more other actions
=gyr,c1
GRID_MIN
the lower bounds for the grid
=2.0,0.2 
GRID_MAX
the upper bounds for the grid
=5,15 
GRID_BIN
the number of bins for the grid
=600,600
SIGMA
the widths of the Gaussian hills
=0.05,0.1  
BIASFACTOR
use well tempered metadynamics and use this bias factor
=5 
HEIGHT
the heights of the Gaussian hills
=0.05
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
...

The METAD action with label mt calculates the following quantities:
 Quantity   
 Description  
mt.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
=t1,t2,t3,t4,t5,t6 
FILE
the name of the file on which to output these quantities
=dihedral 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=mt.bias 
FILE
the name of the file on which to output these quantities
=mt.gbias 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=gyr,c1 
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
=500