PLUMED-NEST

Project ID: plumID:19.042
Source: 2_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

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

The UNITS action with label  calculates somethingenergy: ENERGYCalculate the total potential energy of the simulation box. More details


The ENERGY action with label energy calculates somethingd1: 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=2,3 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=3,4 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 atomsd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=4,5 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=5,6 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 atomsd6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,1 NOPBC ignore the periodic boundary conditions when calculating distances

The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Description  
d6.value
the DISTANCE between this pair of atomscomb1:  COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1,d2,d3,d4,d5,d6 COEFFICIENTS the coefficients of the arguments in your function=0.182,-0.456,0.106,-0.602,0.065,-0.617  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 compbinationUPPER_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=+5.0 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=d6 ATthe positions of the wall=+5.0 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 potentialmetad: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=comb1 PACEthe frequency for hill addition=100 HEIGHTthe heights of the Gaussian hills=5.0 SIGMAthe widths of the Gaussian hills=0.2 GRID_MINthe lower bounds for the grid=-15 GRID_MAXthe upper bounds for the grid=15 GRID_BINthe number of bins for the grid=2000 FILE a file in which the list of added hills is stored=HILLS BIASFACTORuse well tempered metadynamics and use this bias factor=80 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0

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=1
PRINTPrint quantities to a file. More details ...
 ARGthe labels of the values that you would like to print to the file=d1,d2,d3,d4,d5,d6,comb1,metad.*
 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
... PRINT