PLUMED-NEST-TEST-SITE

Click on the labels of the actions for more information on what each action computes

#SETTINGS NREPLICAS=2
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=plumed-common.dat
# The command:
# INCLUDE FILE=plumed-common.dat
# ensures PLUMED loads the contents of the file called plumed-common.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 plumed-common.dat calculates somethingUNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A ENERGYthe units of energy=eV TIMEthe units of time=ps

# CVs
The UNITS action with label  calculates somethingdist:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7345,7346

The DISTANCE action with label dist calculates the following quantities:
 Quantity   
 Description  
dist.value
the DISTANCE between this pair of atomsCOORDINATIONCalculate coordination numbers. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=coord
  GROUPAFirst list of atoms=7345
  GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=2-7343:3
  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1.0 D_0=2.1 NN=4 MM=8}
  NLIST Use a neighbor list to speed up the calculation
  NL_CUTOFFThe cutoff for the neighbor list=10
  NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
... COORDINATION


# metad with multiple walkers
The COORDINATION action with label coord calculates the following quantities:
 Quantity   
 Description  
coord.value
the value of the coordinationMETADUsed 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=metad
  ARGthe labels of the scalars on which the bias will act=dist,coord
  SIGMAthe widths of the Gaussian hills=0.2,0.1
  HEIGHTthe heights of the Gaussian hills=0.025852
  BIASFACTORuse well tempered metadynamics and use this bias factor=5
  TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300
  PACEthe frequency for hill addition=1000
  GRID_MINthe lower bounds for the grid=2,3
  GRID_MAXthe upper bounds for the grid=13,10
  CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
  WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
... METAD

# walls to stay close to associated state
The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
metad.rct
the reweighting factor c(t)UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ...
  ARGthe arguments on which the bias is acting=dist
  ATthe positions of the wall=12
  KAPPAthe force constant for the wall=12.0
  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.
  LABELa label for the action so that its output can be referenced in the input to other actions=wall
... UPPER_WALLS
# --- End of included input --- 
The UPPER_WALLS action with label wall calculates the following quantities:
 Quantity   
 Description  
wall.bias
the instantaneous value of the bias potential
wall.force2
the instantaneous value of the squared force due to this 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=100 FILEthe name of the file on which to output these quantities=COLVAR