PLUMED-NEST

Project ID: plumID:19.015
Source: adsorbed/100_apolar/plumed_restart.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 321##########

#torsion1 between vector1 C2,C1 and axis C2,C10 and vector2 C10,C11 
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
=10564,10563 
AXIS
two atoms that define an axis
=10564,10572 
VECTOR2
two atoms that define a vector
=10572,10573

#torsion2 between vector1 C10,C7 and axis C10,C11 and vector2 C11,C12 
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
=10572,10569 
AXIS
two atoms that define an axis
=10572,10573 
VECTOR2
two atoms that define a vector
=10573,10574

pseudobulkThe CENTER_FAST action with label pseudobulk calculates the following quantities:
 Quantity   
 Type   
 Description  
pseudobulk
atoms
virtual atom calculated by CENTER_FAST action: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=5380-5412,6139-6171,5776-5808,5578-5610,4324-4356,5116-5148,4852-4884,4588-4620,5314-5346,6106-6138,5710-5742,5512-5544,4258-4290,5050-5082,4786-4818,4522-4554,5875-5907,6073-6105,6007-6039,5941-5973,4456-4488,5248-5280,4984-5016,4720-4752,5446-5478,6172-6204,5842-5874,5644-5676,4390-4422,5182-5214,4918-4950,4654-4686,6238-6270,5743-5775,5545-5577,5347-5379,4555-4587,4291-4323,5083-5115,4819-4851,6205-6237,5677-5709,5479-5511,5281-5312,4489-4521,4225-4257,5017-5049,4753-4785,6304-6336,6040-6072,5974-6006,5908-5940,4687-4719,4423-4455,5215-5247,4951-4983,6271-6303,5809-5841,5611-5643,5413-5445,4621-4653,4357-4389,5149-5181,4885-4917

mymolThe CENTER_FAST action with label mymol calculates the following quantities:
 Quantity   
 Type   
 Description  
mymol
atoms
virtual atom calculated by CENTER_FAST action: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=10566-10569

dThe DISTANCE action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d.x
scalar
the x-component of the vector connecting the two atoms
d.y
scalar
the y-component of the vector connecting the two atoms
d.z
scalar
the z-component of the vector connecting the two atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=mymol,pseudobulk 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=d.z 
AT
the positions of the wall
=3.7 
KAPPA
the force constant for the wall
=500.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.force2
scalar
the instantaneous value of the squared force due to this bias potential
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=d.z 
AT
the positions of the wall
=3.4 
KAPPA
the force constant for the wall
=500.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lwallThe LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall.bias
scalar
the instantaneous value of the bias potential
lwall.force2
scalar
the instantaneous value of the squared force due to this bias potential

#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
=0.96
PACE
the frequency for hill addition
=500
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10.0
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

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,d.z,metad.bias,uwall.bias,lwall.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