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 somethingLi: 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 Li 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
#c1: COORDINATIONNUMBER SPECIESA=N SPECIESB=Li R_0=4.0 NN=6 MM=12 MAX={BETA=0.05} MIN={BETA=20.0} MEAN
#c2: COORDINATIONNUMBER SPECIESA=N SPECIESB=Na R_0=4.0 NN=6 MM=12 MAX={BETA=0.05} MIN={BETA=20.0} MEAN
The DISTANCE action with label dn calculates the following quantities:
 Quantity   
 Description  
dn.value
the DISTANCE between this pair of 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_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. 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=180
   RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
   #EXCLUDED_REGION=t1
... OPES_METAD

The OPES_METAD 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