PLUMED-NEST

Project ID: plumID:21.023
Source: Data-mb/mb-wtm-bf4/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

INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=./MuellerBrown-Potential.dat
# The command:
# INCLUDE FILE=./MuellerBrown-Potential.dat
# ensures PLUMED loads the contents of the file called ./MuellerBrown-Potential.dat
# The contents of this file are shown below (click the red comment to hide them).
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
The INCLUDE action with label ./MuellerBrown-Potential.dat calculates somethingUNITSThis command sets the internal units for the code. More details NATURAL use natural units

# Müller-Brown potential, sum of four terms
#-200*exp( -(x-1)^2 -10*y^2 )
#-100*exp( -x^2 -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 )
# Shifted by 146.699489200588 to have a zero value 
# at the global minimum ( -0.558 , 1.442 )
# Minima: ( -0.558 , 1.442 ) [ Value: 0.0 ]
#         (  0.623 , 0.028 ) [ Value: 38.532839 ]
#         ( -0.050 , 0.467 ) [ Value: 65.931740 ] 
# Saddle Points : ( -0.822 ,  0.624 ) [ Value: 106.034644 ]
#                 ( -0.212 ,  0.293 ) [ Value: 88.435607 ]
# Can be scaled via the scaling_factor 
# (above values for minima and saddle points are then scaled)

The UNITS action with label  calculates somethingscaling_factor: CONSTANTCreate a constant value that can be passed to actions More details VALUEthe single number that you would like to store=0.2

The CONSTANT action with label scaling_factor calculates the following quantities:
 Quantity   
 Description  
scaling_factor.value
the constant value that was read from the plumed inputp: 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
The DISTANCE action with label p calculates the following quantities:
 Quantity   
 Description  
p.x
the x-component of the vector connecting the two atoms
p.y
the y-component of the vector connecting the two atoms
p.z
the z-component of the vector connecting the two atoms
p.value
the DISTANCE between this pair of atomsCUSTOMCalculate 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=pot
 ARGthe values input to this function=p.x,p.y,scaling_factor 
 VARthe names to give each of the arguments in the function=x,y,sf
 FUNCthe function you wish to evaluate=sf*(-200*exp(-(x-1)^2-10*y^2)-100*exp(-x^2-10*(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)+146.699489200588)
 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO 
... CUSTOM
The CUSTOM action with label pot calculates the following quantities:
 Quantity   
 Description  
pot.value
an arbitrary functionbv: 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=pot
# --- End of included input --- 
The BIASVALUE action with label bv calculates the following quantities:
 Quantity   
 Description  
bv.bias
the instantaneous value of the bias potential
bv._bias
one or multiple instances of this quantity can be referenced elsewhere in the input fileMETADUsed to performed metadynamics on one or more collective variables. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=mtd

  ARGthe labels of the scalars on which the bias will act=p.x,p.y
  PACEthe frequency for hill addition=100
  SIGMAthe widths of the Gaussian hills=0.1,0.1
  HEIGHTthe heights of the Gaussian hills=1.5

  TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=1
 
  BIASFACTORuse well tempered metadynamics and use this bias factor=4
  GRID_MINthe lower bounds for the grid=-5,-5
  GRID_MAXthe upper bounds for the grid=5,5
  GRID_BINthe number of bins for the grid=500,500
  CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
  RCT_USTRIDEthe update stride for calculating the c(t) reweighting factor=1
... METAD

The METAD action with label mtd calculates the following quantities:
 Quantity   
 Description  
mtd.bias
the instantaneous value of the bias potential
mtd.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
mtd.rct
the reweighting factor c(t)w: REWEIGHT_METADCalculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. More details TEMPthe system temperature=1

The REWEIGHT_METAD action with label w calculates the following quantities:
 Quantity   
 Description  
w.value
the weight to use for this frame to negate the effect the metadynamics biasPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=colvar.data STRIDE the frequency with which the quantities of interest should be output=200