PLUMED-NEST

Project ID: plumID:19.015
Source: surface/100_polar/plumed_kinetics.dat
Originally used with PLUMED version: 2.3
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

#######IBU 28##########


#torsion1 between vector C1,C2 and C10,C11 with axis C2,C10
t1: TORSIONCalculate one or multiple torsional angles. More details VECTOR1You should use VECTORA instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=895,894 AXIStwo atoms that define an axis=895,903 VECTOR2You should use VECTORB instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=903,904

#torsion2 between vector C7,C10 and C11,C12 with axis C10,C11
The TORSION action with label t1 calculates the following quantities:
 Quantity   
 Description  
t1.value
the TORSION involving these atomst2: TORSIONCalculate one or multiple torsional angles. More details VECTOR1You should use VECTORA instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=903,900 AXIStwo atoms that define an axis=903,904 VECTOR2You should use VECTORB instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=904,905

#metadynamics
The TORSION action with label t2 calculates the following quantities:
 Quantity   
 Description  
t2.value
the TORSION involving these atomsMETADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=t1,t2
SIGMAthe widths of the Gaussian hills=0.1,0.1
HEIGHTthe heights of the Gaussian hills=0.24
PACEthe frequency for hill addition=1000
BIASFACTORuse well tempered metadynamics and use this bias factor=5.0
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0
LABELa label for the action so that its output can be referenced in the input to other actions=metad
FILE a file in which the list of added hills is stored=HILLS
GRID_MINthe lower bounds for the grid=-pi,-pi
GRID_MAXthe upper bounds for the grid=pi,pi
GRID_BINthe number of bins for the grid=350,350
... METAD


The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialCOMMITTORDoes a committor analysis. More details ...
  ARGthe labels of the values which is being used to define the committor surface=t1,t2

#C1 basin
  BASIN_LL1List of lower limits for basin #=-3.15,-3.15
  BASIN_UL1List of upper limits for basin #=-2.3,-2.85
  BASIN_LL2List of lower limits for basin #=-3.15,3.13
  BASIN_UL2List of upper limits for basin #=-2.3,3.15
  BASIN_LL3List of lower limits for basin #=3.13,3.13
  BASIN_UL3List of upper limits for basin #=3.15,3.15
  BASIN_LL4List of lower limits for basin #=3.13,-3.15
  BASIN_UL4List of upper limits for basin #=3.15,-2.85
  
#C2 basin
   BASIN_LL5List of lower limits for basin #=-2.7,-1.3
   BASIN_UL5List of upper limits for basin #=-1.9,-1.0

#C3 basin
   BASIN_LL6List of lower limits for basin #=-2.7,0.9
   BASIN_UL6List of upper limits for basin #=-2.3,1.2

#C4 basin
   BASIN_LL7List of lower limits for basin #=-0.1,-3.15
   BASIN_UL7List of upper limits for basin #=0.85,-2.85
   BASIN_LL8List of lower limits for basin #=-0.1,3.13
   BASIN_UL8List of upper limits for basin #=0.85,3.15

#C5 basin
#   BASIN_LL5=0.5,-1.3
#   BASIN_UL5=1.3,-1.0

#C6 basin
   BASIN_LL9List of lower limits for basin #=0.5,0.9
   BASIN_UL9List of upper limits for basin #=1.0,1.2
  
... COMMITTOR


The COMMITTOR action with label  calculates somethingPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=t1,t2,metad.bias STRIDE the frequency with which the quantities of interest should be output=10 FILEthe name of the file on which to output these quantities=COLVAR