PLUMED-NEST-TEST-SITE

Project ID: plumID:21.021
Source: unbiased_inputs/2d/plumed.dat
Originally used with PLUMED version: 2.7-mod
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

#
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=Bohr ENERGYthe units of energy=Ha 

The UNITS action with label  calculates somethingd1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1.x
scalar
the x-component of the vector connecting the two atoms
d1.y
scalar
the y-component of the vector connecting the two atoms
d1.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
#p: POSITION ATOM=1 
#d1: COMBINE COEFFICIENTS=-1.0 ARG=p.x PERIODIC=NO
#d2: COMBINE COEFFICIENTS=-1.0 ARG=p.y PERIODIC=NO

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=d1.x,d1.y VARthe names to give each of the arguments in the function=x0,x1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=30.0*exp(-4.0*(x0-1)^2-4.0*(x1-1)^2)+30.0*exp(-4.0*(x0-1)^2-4.0*(x1+1)^2)+30.0*exp(-4.0*(x0+1)^2-4.0*(x1+1)^2)+30.0/(1.0/((5.0*x0+5.0)^2+(5.0*x1+5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1+5.0)^2+1)+1.0/((5.0*x0-5.0)^2+(5.0*x1-5.0)^2+1)+1.0/((-3.5355339059*x0+3.5355339059*x1)^2+(0.500000000834386*x0+0.500000000834386*x1)^8)+1.0/(1.0*x1^8+(5.0*x0-5.0)^2)+1.0/(1.0*x0^8+(5.0*x1+5.0)^2))

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