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: TORSIONCalculate one or multiple torsional angles. More details VECTOR1two atoms that define a vector=10564,10563 AXIStwo atoms that define an axis=10564,10572 VECTOR2two 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: TORSIONCalculate one or multiple torsional angles. More details VECTOR1two atoms that define a vector=10572,10569 AXIStwo atoms that define an axis=10572,10573 VECTOR2two 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: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe 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: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe 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: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe 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_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d.z ATthe positions of the wall=3.7 KAPPAthe force constant for the wall=500.0 LABELa 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_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d.z ATthe positions of the wall=3.4 KAPPAthe force constant for the wall=500.0 LABELa 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
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=0.96
PACEthe frequency for hill addition=500
BIASFACTORuse well tempered metadynamics and use this bias factor=10.0
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

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=t1,t2,d.z,metad.bias,uwall.bias,lwall.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