PLUMED-NEST-TEST-SITE

Project ID: plumID:23.039
Source: fullerene/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. 
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=nvt.pdb
# bias the distance of the 'methane molecule' from the center of the box
The MOLINFO action with label  calculates somethingc1The CENTER_FAST action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=8121-9020 NOPBC ignore the periodic boundary conditions when calculating distances
c2The CENTER_FAST action with label c2 calculates the following quantities:
 Quantity   
 Type   
 Description  
c2
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=9021-9080
d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1.x
scalar
the x-component of the vector connecting the two atoms
d1.y
scalar
the y-component of the vector connecting the two atoms
d1.z
scalar
the z-component of the vector connecting the two atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c1,c2 COMPONENTS calculate the x, y and z components of the distance separately and store them as label
tmpThe COMBINE action with label tmp calculates the following quantities:
 Quantity   
 Type   
 Description  
tmp
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1.x,d1.y POWERS the powers to which you are raising each of the arguments in your function=2,2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO 
rhoThe COMBINE action with label rho calculates the following quantities:
 Quantity   
 Type   
 Description  
rho
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=tmp POWERS the powers to which you are raising each of the arguments in your function=0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO 
# since I don't see a spring constant defined in the SI of the paper,
# I will use a spring constant of 2 kT
uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1.z ATthe positions of the wall=2.1 KAPPAthe force constant for the wall=100000.0 EXP the powers for the walls=4
pThe RESTRAINT action with label p calculates the following quantities:
 Quantity   
 Type   
 Description  
p.bias
scalar
the instantaneous value of the bias potential
p.force2
scalar
the instantaneous value of the squared force due to this bias potential: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=rho ATthe position of the restraint=0.0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=1000.0
p: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=rho ATthe position of the restraint=0.0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=1000.0  SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
metad.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
metad.rct
scalar
the reweighting factor c(t).: METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
   ARGthe labels of the scalars on which the bias will act=d1.z
   # Deposit a Gaussian every 300 time steps, with initial height equal to 2.0 kJ/mol
   PACEthe frequency for hill addition=300 HEIGHTthe heights of the Gaussian hills=2.0
   # the bias factor should be chosen wisely
   BIASFACTORuse well tempered metadynamics and use this bias factor=15 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0
   # Gaussian width (sigma) should be chosen based on CV fluctuation in unbiased run
   SIGMAthe widths of the Gaussian hills=0.03
   #Gaussians will be written to file and also stored on grid
   GRID_MINthe lower bounds for the grid=-1 GRID_MAXthe upper bounds for the grid=5
   CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
...
metad: METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
   ARGthe labels of the scalars on which the bias will act=d1.z
   # Deposit a Gaussian every 300 time steps, with initial height equal to 2.0 kJ/mol
   PACEthe frequency for hill addition=300 HEIGHTthe heights of the Gaussian hills=2.0
   # the bias factor should be chosen wisely
   BIASFACTORuse well tempered metadynamics and use this bias factor=15 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0
   # Gaussian width (sigma) should be chosen based on CV fluctuation in unbiased run
   SIGMAthe widths of the Gaussian hills=0.03
   #Gaussians will be written to file and also stored on grid
   GRID_MINthe lower bounds for the grid=-1 GRID_MAXthe upper bounds for the grid=5
   CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
 FILE a file in which the list of added hills is stored=HILLS
...
DUMPMASSCHARGEDump masses and charges on a selected file. More details FILEfile on which to output charges and masses=mcfile
# Print both collective variables and the value of the bias potential on COLVAR file
PRINTPrint 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