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 
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=10564,10563 AXIStwo atoms that define an axis=10564,10572 VECTOR2You should use VECTORB instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=10572,10573

#torsion2 between vector1 C10,C7 and axis C10,C11 and vector2 C11,C12 
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=10572,10569 AXIStwo atoms that define an axis=10572,10573 VECTOR2You should use VECTORB instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=10573,10574

The TORSION action with label t2 calculates the following quantities:
 Quantity   
 Description  
t2.value
the TORSION involving these atomspseudobulk: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=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

The CENTER action with label pseudobulk calculates the following quantities:
 Quantity   
 Description  
pseudobulk.value
the position of the center of massmymol: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=10566-10569

The CENTER action with label mymol calculates the following quantities:
 Quantity   
 Description  
mymol.value
the position of the center of massd: 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
The DISTANCE action with label d calculates the following quantities:
 Quantity   
 Description  
d.x
the x-component of the vector connecting the two atoms
d.y
the y-component of the vector connecting the two atoms
d.z
the z-component of the vector connecting the two atoms
d.value
the DISTANCE between this pair of atomsUPPER_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=uwall
The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentialLOWER_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=lwall

#metadynamics
The LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Description  
lwall.bias
the instantaneous value of the bias potential
lwall.force2
the instantaneous value of the squared force due to this bias potentialMETADUsed 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=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 potentialPRINTPrint 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