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: 
TORSION
Calculate a torsional angle. More details
 
VECTOR1
two atoms that define a vector
=10168,10167 
AXIS
two atoms that define an axis
=10168,10176 
VECTOR2
two 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: 
TORSION
Calculate a torsional angle. More details
 
VECTOR1
two atoms that define a vector
=10176,10173 
AXIS
two atoms that define an axis
=10176,10177 
VECTOR2
two atoms that define a vector
=10177,10178

#metadynamics
METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
ARG
the input for this action is the scalar output from one or more other actions
=t1,t2
SIGMA
the widths of the Gaussian hills
=0.1,0.1
HEIGHT
the heights of the Gaussian hills
=0.24
PACE
the frequency for hill addition
=1000
BIASFACTOR
use well tempered metadynamics and use this bias factor
=5.0
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0
LABEL
a 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_MIN
the lower bounds for the grid
=-pi,-pi
GRID_MAX
the upper bounds for the grid
=pi,pi
GRID_BIN
the number of bins for the grid
=350,350
... METAD


COMMITTOR
Does a committor analysis. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=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_LL1
List of lower limits for basin #
=-2.7,-1.3
   
BASIN_UL1
List of upper limits for basin #
=-1.9,-1.0

#C3 basin
   
BASIN_LL2
List of lower limits for basin #
=-2.7,0.9
   
BASIN_UL2
List of upper limits for basin #
=-2.3,1.2

#C4 basin
   
BASIN_LL3
List of lower limits for basin #
=-0.1,-3.15
   
BASIN_UL3
List of upper limits for basin #
=0.85,-2.85
   
BASIN_LL4
List of lower limits for basin #
=-0.1,3.13
   
BASIN_UL4
List of upper limits for basin #
=0.85,3.15

#C5 basin
   
BASIN_LL5
List of lower limits for basin #
=0.5,-1.3
   
BASIN_UL5
List of upper limits for basin #
=1.3,-1.0

#C6 basin
   
BASIN_LL6
List of lower limits for basin #
=0.5,0.9
   
BASIN_UL6
List of upper limits for basin #
=1.0,1.2
  
... COMMITTOR


The COMMITTOR action with label  calculates something
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=t1,t2,metad.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=10 
FILE
the name of the file on which to output these quantities
=COLVAR