PLUMED-NEST-TEST-SITE

Project ID: plumID:22.006
Source: analysis/new_cvs.plumed
Originally used with PLUMED version: 2.5
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

# groups.txt is generated by parse_atoms.py
# an example groups.txt file is included
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details FILEfile to be included=groups.txt


The INCLUDE action with label  calculates somethingc1com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=c1
The COM action with label c1com calculates somethingc2com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=c2
The COM action with label c2com calculates somethingc3com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=c3
The COM action with label c3com calculates somethingc4com: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=c4

The COM action with label c4com calculates somethingdist: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPCalculate the distance between each distinct pair of atoms in the group=c1com,c2com,c3com,c4com MEAN calculate the mean of all the quantities MINcalculate the minimum value={BETA=0.1}
The DISTANCES action with label dist calculates the following quantities:
 Quantity   
 Description  
dist.min
the minimum colvar
dist.mean
the mean of the colvars
dist.value
the DISTANCES between the each pair of atoms that were specifieddist2: 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=c1com,c2com GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=c3com,c4com MEAN calculate the mean of all the quantities

The DISTANCES action with label dist2 calculates the following quantities:
 Quantity   
 Description  
dist2.mean
the mean of the colvars
dist2.value
the DISTANCES between the each pair of atoms that were specifiedrg1: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=c1
The GYRATION action with label rg1 calculates the following quantities:
 Quantity   
 Description  
rg1.value
the radius that was computed from the weightsrg2: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=c2
The GYRATION action with label rg2 calculates the following quantities:
 Quantity   
 Description  
rg2.value
the radius that was computed from the weightsrg3: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=c3
The GYRATION action with label rg3 calculates the following quantities:
 Quantity   
 Description  
rg3.value
the radius that was computed from the weightsrg4: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=c4

The GYRATION action with label rg4 calculates the following quantities:
 Quantity   
 Description  
rg4.value
the radius that was computed from the weightsrg: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=rg1,rg2,rg3,rg4 NORMALIZE normalize all the coefficients so that in total they are equal to one PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

The COMBINE action with label rg calculates the following quantities:
 Quantity   
 Description  
rg.value
a linear compbinationMETADUsed to performed metadynamics on one or more collective variables. More details ...
      ARGthe labels of the scalars on which the bias will act=dist.mean,rg PACEthe frequency for hill addition=99999999 BIASFACTORuse well tempered metadynamics and use this bias factor=5 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0 SIGMAthe widths of the Gaussian hills=0.05,0.01
      GRID_MINthe lower bounds for the grid=0,0 GRID_MAXthe upper bounds for the grid=5,1.5  GRID_BINthe number of bins for the grid=500,500 HEIGHTthe heights of the Gaussian hills=5
# Uncomment line when HILLS file is present      RESTART=YES
... METAD

bias: REWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More details TEMPthe system temperature=300.0

The REWEIGHT_BIAS action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.value
the weight to use for this frame to negate the effect the biasHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
  ARGthe quantities that are being used to construct the histogram=dist.min,rg
  GRID_MIN the lower bounds for the grid=0.0,0.0
  GRID_MAX the upper bounds for the grid=5.0,1.0
  GRID_BINthe number of bins for the grid=500,500
  BANDWIDTHthe bandwidths for kernel density esimtation=0.1,0.1
  LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias
  LABELa label for the action so that its output can be referenced in the input to other actions=hB
... HISTOGRAM

The HISTOGRAM action with label hB calculates the following quantities:
 Quantity   
 Description  
hB.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
  ARGthe quantities that are being used to construct the histogram=dist2.mean
  GRID_MIN the lower bounds for the grid=0.0
  GRID_MAX the upper bounds for the grid=5.0
  GRID_BINthe number of bins for the grid=1000
  BANDWIDTHthe bandwidths for kernel density esimtation=0.05
  LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias
  LABELa label for the action so that its output can be referenced in the input to other actions=hR
... HISTOGRAM

#PRINT STRIDE=1 FILE=weights.dat ARG=bias


#ff: CONVERT_TO_FES GRID=hB TEMP=300
The HISTOGRAM action with label hR calculates the following quantities:
 Quantity   
 Description  
hR.value
the estimate of the histogram as a function of the argument that was obtainedffr: CONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=hR TEMPthe temperature at which you are operating=300

#DUMPGRID GRID=ff FILE=fes.dat
The CONVERT_TO_FES action with label ffr calculates the following quantities:
 Quantity   
 Description  
ffr.value
the free energy surfaceDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=ffr FILE the file on which to write the grid=fes_np_dist.dat