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

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UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A

The UNITS action with label  calculates somethingt1The TORSION action with label t1 calculates the following quantities:
 Quantity   
 Type   
 Description  
t1
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=5,7,9,15
t2The TORSION action with label t2 calculates the following quantities:
 Quantity   
 Type   
 Description  
t2
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=7,9,15,17
t3The TORSION action with label t3 calculates the following quantities:
 Quantity   
 Type   
 Description  
t3
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=15,17,19,25
t4The TORSION action with label t4 calculates the following quantities:
 Quantity   
 Type   
 Description  
t4
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=17,19,25,27
t5The TORSION action with label t5 calculates the following quantities:
 Quantity   
 Type   
 Description  
t5
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=25,27,29,35
t6The TORSION action with label t6 calculates the following quantities:
 Quantity   
 Type   
 Description  
t6
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=27,29,35,37

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=1-42
gyrThe GYRATION action with label gyr calculates the following quantities:
 Quantity   
 Type   
 Description  
gyr
scalar
the radius of gyration: GYRATIONCalculate 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 ATOMSthe 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

hyThe GROUP action with label hy calculates the following quantities:
 Quantity   
 Type   
 Description  
hy
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=8,18,28,38
oxThe GROUP action with label ox calculates the following quantities:
 Quantity   
 Type   
 Description  
ox
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=6,16,26,36
c1The COORDINATION action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=ox GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=hy  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=3 D_MAX=4}

mtThe METAD action with label mt calculates the following quantities:
 Quantity   
 Type   
 Description  
mt.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
PACEthe frequency for hill addition=500
ARGthe labels of the scalars on which the bias will act=gyr,c1
GRID_MINthe lower bounds for the grid=2.0,0.2 GRID_MAXthe upper bounds for the grid=5,15 GRID_BINthe number of bins for the grid=600,600
SIGMAthe widths of the Gaussian hills=0.05,0.1  BIASFACTORuse well tempered metadynamics and use this bias factor=5 HEIGHTthe heights of the Gaussian hills=0.05
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300
...
mt: METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
PACEthe frequency for hill addition=500
ARGthe labels of the scalars on which the bias will act=gyr,c1
GRID_MINthe lower bounds for the grid=2.0,0.2 GRID_MAXthe upper bounds for the grid=5,15 GRID_BINthe number of bins for the grid=600,600
SIGMAthe widths of the Gaussian hills=0.05,0.1  BIASFACTORuse well tempered metadynamics and use this bias factor=5 HEIGHTthe heights of the Gaussian hills=0.05
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300
 FILE a file in which the list of added hills is stored=HILLS
...

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=t1,t2,t3,t4,t5,t6 FILEthe name of the file on which to output these quantities=dihedral STRIDE the frequency with which the quantities of interest should be output=500
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=mt.bias FILEthe 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=gyr,c1 FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=500