PLUMED-NEST

Project ID: plumID:19.050
Source: plumed_metad.dat
Originally used with PLUMED version: not specified
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

# The two lines below instruct PLUMED to calculate the distance between
# the adsorbate and the isosurface.  Notice how, as discussed in the main text,
# only a subset of the atoms in the membrane are used when we calculate the
# density as this reduces the computational expense.
contThe DISTANCE_FROM_CONTOUR action with label cont calculates the following quantities:
 Quantity   
 Type   
 Description  
cont.thickness
scalar
the distance between the two contours on the line from the reference atom
cont.dist1
scalar
the distance between the reference atom and the nearest contour
cont.dist2
scalar
the distance between the reference atom and the other contour
cont.qdist
scalar
the differentiable (squared) distance between the two contours (see above): DISTANCE_FROM_CONTOURCalculate the perpendicular distance from a Willard-Chandler dividing surface. This action has hidden defaults. More details ...
  POSITIONSthe positions of the atoms that we are calculating the contour from=2-2400:12,10-2400:12 ATOMThe atom whose perpendicular distance we are calculating from the contour=2413 BANDWIDTHthe bandwidths for kernel density esimtation=3.0,3.0,3.0 DIRthe direction perpendicular to the contour that you are looking for=z CONTOURthe value we would like for the contour=0.42
...
cont: DISTANCE_FROM_CONTOURCalculate the perpendicular distance from a Willard-Chandler dividing surface. This action uses the defaults shown here. More details ...
  POSITIONSthe positions of the atoms that we are calculating the contour from=2-2400:12,10-2400:12 ATOMThe atom whose perpendicular distance we are calculating from the contour=2413 BANDWIDTHthe bandwidths for kernel density esimtation=3.0,3.0,3.0 DIRthe direction perpendicular to the contour that you are looking for=z CONTOURthe value we would like for the contour=0.42
 KERNEL the kernel function you are using=GAUSSIAN CUTOFF the cutoff at which to stop evaluating the kernel functions is set equal to sqrt(2*x)*bandwidth in each direction where x is this number=6.25 TOLERANCE this parameter is used to manage periodic boundary conditions=0.1
...
# This command instructs PLUMED to construct a metadynamics bias that is a
# function of the CV that is used in the main text.  In order to reduce the
# computational expense this bias is stored on a grid.  Furthermore, adaptive
# hills are used to ensure faster convergence of the final free energy surface
mmThe METAD action with label mm calculates the following quantities:
 Quantity   
 Type   
 Description  
mm.bias
scalar
the instantaneous value of the bias potential: 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=cont.qdist SIGMAthe widths of the Gaussian hills=0.5 HEIGHTthe heights of the Gaussian hills=1.3 PACEthe frequency for hill addition=100 BIASFACTORuse well tempered metadynamics and use this bias factor=25 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=325
  GRID_MINthe lower bounds for the grid=-15.0 GRID_MAXthe upper bounds for the grid=100.0 GRID_BINthe number of bins for the grid=115000
  ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=GEOM SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.05 SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=6.00
...
mm: 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=cont.qdist SIGMAthe widths of the Gaussian hills=0.5 HEIGHTthe heights of the Gaussian hills=1.3 PACEthe frequency for hill addition=100 BIASFACTORuse well tempered metadynamics and use this bias factor=25 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=325
  GRID_MINthe lower bounds for the grid=-15.0 GRID_MAXthe upper bounds for the grid=100.0 GRID_BINthe number of bins for the grid=115000
  ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=GEOM SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.05 SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=6.00
 FILE a file in which the list of added hills is stored=HILLS
...
# This command instructs PLUMED to add a restraint that prevents the collective
# variable from taking high values. This restraint thus prevents the adsorbate
# from moving too far from the membrane surface.
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=cont.qdist ATthe positions of the wall=50.0 KAPPAthe force constant for the wall=1.0 EXP the powers for the walls=2
# This command prints the value of the collective variable and the metadynamics
# bias to a file called colvar
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cont.*,mm.* STRIDE the frequency with which the quantities of interest should be output=20 FILEthe name of the file on which to output these quantities=colvar