PLUMED-NEST-TEST-SITE

Project ID: plumID:24.005
Source: plumed.dat
Originally used with PLUMED version: 2.7
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

# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
UNITSThis command sets the internal units for the code. More details NATURAL use natural units

The UNITS action with label  calculates somethingpThe 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
CUSTOMCalculate a combination of variables using a custom expression. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=wqThe CUSTOM action with label wq calculates the following quantities:
 Quantity   
 Type   
 Description  
wq
scalar
an arbitrary function
  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
  VARthe names to give each of the arguments in the function=x,y
  FUNCthe function you wish to evaluate=0.15*(146.7-280*exp(-15*(x-1)^2+0*(x-1)*(y-0)-10*(y-0)^2)-170*exp(-1*(x-0.2)^2+0*(x-0)*(y-0.5)-10*(y-0.5)^2)-170*exp(-6.5*(x+0.5)^2+11*(x+0.5)*(y-1.5)-6.5*(y-1.5)^2)+15*exp(0.7*(x+1)^2+0.6*(x+1)*(y-1)+0.7*(y-1)^2))+sin(2.0*pi*x*5)*sin(2.0*pi*y*5)
... CUSTOM
potentialThe BIASVALUE action with label potential calculates the following quantities:
 Quantity   
 Type   
 Description  
potential.bias
scalar
the instantaneous value of the bias potential
potential.wq_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 wq: 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=wq

PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=200 FILEthe name of the file on which to output these quantities=colvar.dat ARGthe labels of the values that you would like to print to the file=p.x,p.y,wq