PLUMED-NEST

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. 
#RESTART
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=0.001  #Amstroeng, kJ/mol, fs

The UNITS action with label  calculates somethingNa: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-1000:1
The GROUP action with label Na calculates somethingN: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1001,1002

The GROUP action with label N calculates somethingdn: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=N
The DISTANCE action with label dn calculates the following quantities:
 Quantity   
 Description  
dn.value
the DISTANCE between this pair of atomsc2: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=N SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=Na R_0The r_0 parameter of the switching function=4.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12 MAXcalculate the maximum value={BETA=0.05} MINcalculate the minimum value={BETA=20.0} MEAN calculate the mean of all the quantities
The COORDINATIONNUMBER action with label c2 calculates the following quantities:
 Quantity   
 Description  
c2.min
the minimum colvar
c2.max
the maximum colvar
c2.mean
the mean of the colvars
c2.value
the coordination numbers of the specified atomsuwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dn ATthe positions of the wall=10.0 KAPPAthe force constant for the wall=1000.0 EXP the powers for the walls=2.0

The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentialOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
   LABELa label for the action so that its output can be referenced in the input to other actions=opes1
   ARGthe labels of the scalars on which the bias will act=dn
   FILE a file in which the list of all deposited kernels is stored=Kernels1.data
   TEMP temperature=600
   PACEthe frequency for kernel deposition=200
   BARRIERthe free energy barrier to be overcome=320
   RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
... OPES_METAD_EXPLORE

The OPES_METAD_EXPLORE action with label opes1 calculates the following quantities:
 Quantity   
 Description  
opes1.bias
the instantaneous value of the bias potential
opes1.rct
estimate of c(t)
opes1.zed
estimate of Z_n
opes1.neff
effective sample size
opes1.nker
total number of compressed kernels used to represent the biasPRINTPrint 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=50 FILEthe name of the file on which to output these quantities=COLVAR
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1