PLUMED-NEST

Project ID: plumID:19.073
Source: Paper2_setup/plumed_aa.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

# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
DISTANCESCalculate the distances between multiple piars of atoms More details LABELa label for the action so that its output can be referenced in the input to other actions=d1 GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1-3,61-63  GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=82,98,114,22,38,54 LOWEST this flag allows you to recover the lowest of these variables LOWMEMIncluding this keyword in the input to this action makes no difference to the calculation performed it was used in older versions of PLUMED and is provided here for back compatibility only
The DISTANCES action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.lowest
the smallest of the colvars
d1.value
the DISTANCES between the each pair of atoms that were specifiedDISTANCESCalculate the distances between multiple piars of atoms More details LABELa label for the action so that its output can be referenced in the input to other actions=d2 GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1-3        GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=61-63              LOWEST this flag allows you to recover the lowest of these variables LOWMEMIncluding this keyword in the input to this action makes no difference to the calculation performed it was used in older versions of PLUMED and is provided here for back compatibility only
The DISTANCES action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.lowest
the smallest of the colvars
d2.value
the DISTANCES between the each pair of atoms that were specifiedCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details LABELa label for the action so that its output can be referenced in the input to other actions=cv1 SPECIESAthe list of atoms for which the symmetry function is being calculated=1-3,61-63 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=23,24,39,40,55,56,83,84,99,100,115,116 R_0The r_0 parameter of the switching function=0.25 MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=0.5 NN=2 MM=4 D_0=0}
The COORDINATIONNUMBER action with label cv1 calculates the following quantities:
 Quantity   
 Description  
cv1.morethan
the number of colvars that have a value more than a threshold
cv1.value
the coordination numbers of the specified atomsENERGYCalculate the total potential energy of the simulation box. More details LABELa label for the action so that its output can be referenced in the input to other actions=ene

The ENERGY action with label ene calculates somethingUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1.lowest ATthe positions of the wall=0.35 KAPPAthe force constant for the wall=150 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=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 potentialLOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1.lowest ATthe positions of the wall=0.15 KAPPAthe force constant for the wall=150 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=lwall

The LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Description  
lwall.bias
the instantaneous value of the bias potential
lwall.force2
the instantaneous value of the squared force due to this bias potentialMETADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=cv1.morethan,ene SIGMAthe widths of the Gaussian hills=0.01,200 HEIGHTthe heights of the Gaussian hills=2.5 PACEthe frequency for hill addition=500
LABELa label for the action so that its output can be referenced in the input to other actions=metad TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=298 BIASFACTORuse well tempered metadynamics and use this bias factor=100 FILE a file in which the list of added hills is stored=hills_aa
GRID_MINthe lower bounds for the grid=-0.5,-200000 GRID_MAXthe upper bounds for the grid=6,-120000 GRID_BINthe number of bins for the grid=526,350 GRID_SPARSE use a sparse grid to store hills
... METAD

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialPRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=100 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_aa.dat

The PRINT action with label  calculates somethingENDPLUMEDTerminate plumed input. More details