PLUMED-NEST

Project ID: plumID:19.067
Source: ache-pwf/plumed-biased.dat
Originally used with PLUMED version: 2.4
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=nm TIMEthe units of time=ps ENERGYthe units of energy=kcal/mol

The UNITS action with label  calculates somethingpwf: PATHMSDThis Colvar calculates path collective variables. More details REFERENCEthe pdb is needed to provide the various milestones=pwf.pdb LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=65

The PATHMSD action with label pwf calculates the following quantities:
 Quantity   
 Description  
pwf.sss
the position on the path
pwf.zzz
the distance from the pathls: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pwf.sss ATthe positions of the wall=1.10 KAPPAthe force constant for the wall=30000 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0
The LOWER_WALLS action with label ls calculates the following quantities:
 Quantity   
 Description  
ls.bias
the instantaneous value of the bias potential
ls.force2
the instantaneous value of the squared force due to this bias potentialus: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pwf.sss ATthe positions of the wall=19.5 KAPPAthe force constant for the wall=30000 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0
The UPPER_WALLS action with label us calculates the following quantities:
 Quantity   
 Description  
us.bias
the instantaneous value of the bias potential
us.force2
the instantaneous value of the squared force due to this bias potentialuz: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pwf.zzz ATthe positions of the wall=0.06 KAPPAthe force constant for the wall=30000 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0

The UPPER_WALLS action with label uz calculates the following quantities:
 Quantity   
 Description  
uz.bias
the instantaneous value of the bias potential
uz.force2
the instantaneous value of the squared force due to this bias potentialMETADUsed 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=meta
  ARGthe labels of the scalars on which the bias will act=pwf.sss
  ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=DIFF 
  SIGMAthe widths of the Gaussian hills=125 
  HEIGHTthe heights of the Gaussian hills=2.0 
  TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 
  BIASFACTORuse well tempered metadynamics and use this bias factor=13
  PACEthe frequency for hill addition=125 
  GRID_MINthe lower bounds for the grid=0.5
  GRID_MAXthe upper bounds for the grid=20.5
  GRID_BINthe number of bins for the grid=1000
... METAD

The METAD action with label meta calculates the following quantities:
 Quantity   
 Description  
meta.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=* 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_pwf FMTthe format that should be used to output real numbers=%12.8f