PLUMED-NEST

Project ID: plumID:19.043
Source: 3_class/meta/plumed.dat
Originally used with PLUMED version: 2.3
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

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UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=0.001  #Amstroeng, fs
The UNITS action with label  calculates somethingRESTARTActivate restart. More details

d1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2 NOPBC ignore the periodic boundary conditions when calculating distances 
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsd2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,3 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsd3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,6 NOPBC ignore the periodic boundary conditions when calculating distances

The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomshc: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=1 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=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=2.0 NN=6 MM=12}

The DISTANCES action with label hc calculates the following quantities:
 Quantity   
 Description  
hc.lessthan
the number of colvars that have a value less than a threshold
hc.value
the DISTANCES between the each pair of atoms that were specifiedd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,4 NOPBC ignore the periodic boundary conditions when calculating distances
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atomsd5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,5 NOPBC ignore the periodic boundary conditions when calculating distances

The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atomsUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1 ATthe positions of the wall=+7.5  KAPPAthe force constant for the wall=150.0 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_1
The UPPER_WALLS action with label uwall_1 calculates the following quantities:
 Quantity   
 Description  
uwall_1.bias
the instantaneous value of the bias potential
uwall_1.force2
the instantaneous value of the squared force due to this bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d2 ATthe positions of the wall=+7.5  KAPPAthe force constant for the wall=150.0 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_2
The UPPER_WALLS action with label uwall_2 calculates the following quantities:
 Quantity   
 Description  
uwall_2.bias
the instantaneous value of the bias potential
uwall_2.force2
the instantaneous value of the squared force due to this bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d3 ATthe positions of the wall=+7.5  KAPPAthe force constant for the wall=150.0 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_3
The UPPER_WALLS action with label uwall_3 calculates the following quantities:
 Quantity   
 Description  
uwall_3.bias
the instantaneous value of the bias potential
uwall_3.force2
the instantaneous value of the squared force due to this bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d4 ATthe positions of the wall=+1.25 KAPPAthe force constant for the wall=500.0 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_4
The UPPER_WALLS action with label uwall_4 calculates the following quantities:
 Quantity   
 Description  
uwall_4.bias
the instantaneous value of the bias potential
uwall_4.force2
the instantaneous value of the squared force due to this bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d5 ATthe positions of the wall=+1.25 KAPPAthe force constant for the wall=500.0 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_5

The UPPER_WALLS action with label uwall_5 calculates the following quantities:
 Quantity   
 Description  
uwall_5.bias
the instantaneous value of the bias potential
uwall_5.force2
the instantaneous value of the squared force due to this bias potentialcomb1:  COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1,d2,d3 COEFFICIENTS the coefficients of the arguments in your function=0.555,-0.810,0.190 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The COMBINE action with label comb1 calculates the following quantities:
 Quantity   
 Description  
comb1.value
a linear compbinationcomb2:  COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1,d2,d3 COEFFICIENTS the coefficients of the arguments in your function=0.600,0.234,-0.765 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

The COMBINE action with label comb2 calculates the following quantities:
 Quantity   
 Description  
comb2.value
a linear compbinationMETADUsed 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=comb1,comb2
 PACEthe frequency for hill addition=50 
 HEIGHTthe heights of the Gaussian hills=2.0 
 SIGMAthe widths of the Gaussian hills=0.2 
 GRID_MINthe lower bounds for the grid=-15,-15
 GRID_MAXthe upper bounds for the grid=15,15
 GRID_BINthe number of bins for the grid=300,300
 FILE a file in which the list of added hills is stored=HILLS
 BIASFACTORuse well tempered metadynamics and use this bias factor=25  
 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0 
 ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=GEOM
... METAD


The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialFLUSHThis 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=10
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=COLVAR ARGthe labels of the values that you would like to print to the file=d1,d2,d3,comb1,comb2,d4,d5,metad.*