PLUMED-NEST-TEST-SITE

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

rnaThe GROUP action with label rna calculates the following quantities:
 Quantity   
 Type   
 Description  
rna
atoms
indices of atoms specified in GROUP: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=1-1687
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=rna

#Dummy atoms 
The WHOLEMOLECULES action with label  calculates somethingcom1The COM action with label com1 calculates the following quantities:
 Quantity   
 Type   
 Description  
com1
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-340,1293-1686
com2The COM action with label com2 calculates the following quantities:
 Quantity   
 Type   
 Description  
com2
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=520-1290
com3The COM action with label com3 calculates the following quantities:
 Quantity   
 Type   
 Description  
com3
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-29,1653-1687
com4The COM action with label com4 calculates the following quantities:
 Quantity   
 Type   
 Description  
com4
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=341-371,1292-1323
com5The COM action with label com5 calculates the following quantities:
 Quantity   
 Type   
 Description  
com5
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=522-552,1257-1291
com6The COM action with label com6 calculates the following quantities:
 Quantity   
 Type   
 Description  
com6
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=867-930

#CVs: d and theta
dThe DISTANCE action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=com1,com2 NOPBC ignore the periodic boundary conditions when calculating distances
thetaThe TORSION action with label theta calculates the following quantities:
 Quantity   
 Type   
 Description  
theta
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=com3,com4,com5,com6

#Activate well-tempered metadynamics 
METADUsed to performed metadynamics on one or more collective variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
metad.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
metad.rct
scalar
the reweighting factor c(t).
ARGthe labels of the scalars on which the bias will act=d,theta
PACEthe frequency for hill addition=500
HEIGHTthe heights of the Gaussian hills=0.6
BIASFACTORuse well tempered metadynamics and use this bias factor=6.0
SIGMAthe widths of the Gaussian hills=0.1,0.2
FILE a file in which the list of added hills is stored=HILLS
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0
GRID_MINthe lower bounds for the grid=1.0,-pi
GRID_MAXthe 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
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=10 ARGthe labels of the values that you would like to print to the file=d,theta,metad.rbias FILEthe name of the file on which to output these quantities=COLVAR