PLUMED-NEST

Project ID: plumID:24.006
Source: chemicalPotentialDifference/plumed.dat
Originally used with PLUMED version: 2.8
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

# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=ps ENERGYthe units of energy=eV
The UNITS action with label  calculates somethingc1: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-3000:3 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=1 D_0=3.5 D_MAX=4.5} LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=2 NN=12 MM=24} LOWMEM this flag does nothing and is present only to ensure back-compatibility
The COORDINATIONNUMBER action with label c1 calculates the following quantities:
 Quantity   
 Description  
c1.lessthan
the number of colvars that have a value less than a threshold
c1.value
the coordination numbers of the specified atomsmt: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=c1.lessthan ...
 PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=0.02 BIASFACTORuse well tempered metadynamics and use this bias factor=50   
 SIGMAthe widths of the Gaussian hills=1 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=373  
 FILE a file in which the list of added hills is stored=HILLS GRID_MINthe lower bounds for the grid=0 GRID_MAXthe upper bounds for the grid=50 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... 
The METAD action with label mt calculates the following quantities:
 Quantity   
 Description  
mt.bias
the instantaneous value of the bias potential
mt.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
mt.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=c1.lessthan ATthe positions of the wall=30.0 KAPPAthe force constant for the wall=0.1 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=uwall
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 potentialPRINTPrint 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 STRIDE the frequency with which the quantities of interest should be output=100