Project ID: plumID:22.020
Source: FES/plumed.dat
Originally used with PLUMED version: 2.4
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
tested onv2.9
tested onmaster
rna: 
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
=1-1687

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
=rna

#Dummy atoms 
com1: 
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
=1-340,1293-1686
com2: 
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
=520-1290
com3: 
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
=1-29,1653-1687
com4: 
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
=341-371,1292-1323
com5: 
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
=522-552,1257-1291
com6: 
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
=867-930

#CVs: d and theta
d: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=com1,com2 
NOPBC
 ignore the periodic boundary conditions when calculating distances

theta: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=com3,com4,com5,com6

#Activate well-tempered metadynamics 

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,theta

PACE
the frequency for hill addition
=500

HEIGHT
the heights of the Gaussian hills
=0.6

BIASFACTOR
use well tempered metadynamics and use this bias factor
=6.0

SIGMA
the widths of the Gaussian hills
=0.1,0.2

FILE
 a file in which the list of added hills is stored
=HILLS

TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0

GRID_MIN
the lower bounds for the grid
=1.0,-pi

GRID_MAX
the upper bounds for the grid
=10.0,pi

CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]

... METAD

#Print CVs and bias

PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=10 
ARG
the input for this action is the scalar output from one or more other actions
=d,theta,metad.rbias 
FILE
the name of the file on which to output these quantities
=COLVAR