PLUMED-NEST

Project ID: plumID:24.013
Source: plumed_2D_with_US.dat
Originally used with PLUMED version: 2.9
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

pThe DISTANCE action with label p calculates the following quantities:
 Quantity   
 Type   
 Description  
p.x
scalar
the x-component of the vector connecting the two atoms
p.y
scalar
the y-component of the vector connecting the two atoms
p.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=1,2 COMPONENTS calculate the x, y and z components of the distance separately and store them as label
ffThe MATHEVAL action with label ff calculates the following quantities:
 Quantity   
 Type   
 Description  
ff
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=p.x,p.y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=(1.34549*x^4+1.90211*x^3*y+3.92705*x^2*y^2-6.44246*x^2-1.90211*x*y^3+5.58721*x*y+1.33481*x+1.34549*y^4-5.55754*y^2+0.904586*y+18.5598)
bbThe BIASVALUE action with label bb calculates the following quantities:
 Quantity   
 Type   
 Description  
bb.bias
scalar
the instantaneous value of the bias potential
bb.ff_bias
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named ff: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=ff
METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=p.x,p.y PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.1,0.1 HEIGHTthe heights of the Gaussian hills=1 GRID_MINthe lower bounds for the grid=-4,-4 GRID_MAXthe upper bounds for the grid=4,4 GRID_BINthe number of bins for the grid=400,400 BIASFACTORuse well tempered metadynamics and use this bias factor=10 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=120 FILE a file in which the list of added hills is stored=HILLSinve_HP
The METAD action with label  calculates the following quantities:
 Quantity   
 Description  
.bias
the instantaneous value of the bias potentialRESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=p.x,p.y ATthe position of the restraint=0.8,0.8 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=10,10 LABELa label for the action so that its output can be referenced in the input to other actions=restraintThe RESTRAINT action with label restraint calculates the following quantities:
 Quantity   
 Type   
 Description  
restraint.bias
scalar
the instantaneous value of the bias potential
restraint.force2
scalar
the instantaneous value of the squared force due to this bias potential 
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=p.x,p.y ATthe position of the restraint=0.8,0.8 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=10,10 LABELa label for the action so that its output can be referenced in the input to other actions=restraint  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0,0.0
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=positioninve_HP ARGthe labels of the values that you would like to print to the file=p.x,p.y STRIDE the frequency with which the quantities of interest should be output=50