PLUMED-NEST

Project ID: plumID:19.015
Source: surface/100_apolar/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 309##########

#torsion1 between vector C1,C2 and C10,C11 with axis C2,C10
t1The 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 VECTOR1two atoms that define a vector=10168,10167 AXIStwo atoms that define an axis=10168,10176 VECTOR2two atoms that define a vector=10176,10177

#torsion2 between vector C7,C10 and C11,C12 with axis C10,C11
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 VECTOR1two atoms that define a vector=10176,10173 AXIStwo atoms that define an axis=10176,10177 VECTOR2two atoms that define a vector=10177,10178

#metadynamics
METADUsed 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=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
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


COMMITTORDoes a committor analysis. More details ...
  ARGthe labels of the values which is being used to define the committor surface=t1,t2

#C1 basin
#   BASIN_LL1=-3.15,-3.15
#   BASIN_UL1=-2.3,-2.85
#   BASIN_LL2=-3.15,3.13
#   BASIN_UL2=-2.3,3.15
#   BASIN_LL3=3.13,3.13
#   BASIN_UL3=3.15,3.15
#   BASIN_LL4=3.13,-3.15
#   BASIN_UL4=3.15,-2.85
  
#C2 basin
   BASIN_LL1List of lower limits for basin #=-2.7,-1.3
   BASIN_UL1List of upper limits for basin #=-1.9,-1.0

#C3 basin
   BASIN_LL2List of lower limits for basin #=-2.7,0.9
   BASIN_UL2List of upper limits for basin #=-2.3,1.2

#C4 basin
   BASIN_LL3List of lower limits for basin #=-0.1,-3.15
   BASIN_UL3List of upper limits for basin #=0.85,-2.85
   BASIN_LL4List of lower limits for basin #=-0.1,3.13
   BASIN_UL4List of upper limits for basin #=0.85,3.15

#C5 basin
   BASIN_LL5List of lower limits for basin #=0.5,-1.3
   BASIN_UL5List of upper limits for basin #=1.3,-1.0

#C6 basin
   BASIN_LL6List of lower limits for basin #=0.5,0.9
   BASIN_UL6List 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