PLUMED-NEST

Project ID: plumID:24.036
Source: DIDE/plumed.dat
Originally used with PLUMED version: 2.4
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

WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-6951

The WHOLEMOLECULES action with label  calculates somethingd0:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5825,6817
The DISTANCE action with label d0 calculates the following quantities:
 Quantity   
 Description  
d0.value
the DISTANCE between this pair of atomsang0: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=6868,6865,6804


The ANGLE action with label ang0 calculates the following quantities:
 Quantity   
 Description  
ang0.value
the ANGLE involving these atomsHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
#UPDATE_FROM=500
  ARGthe quantities that are being used to construct the histogram=d0
  GRID_MIN the lower bounds for the grid=0.2   GRID_MAX the upper bounds for the grid=1.2   GRID_BINthe number of bins for the grid=100
  BANDWIDTHthe bandwidths for kernel density esimtation=0.01
  LABELa label for the action so that its output can be referenced in the input to other actions=hh0
... HISTOGRAM

The HISTOGRAM action with label hh0 calculates the following quantities:
 Quantity   
 Description  
hh0.value
the estimate of the histogram as a function of the argument that was obtainedff0: 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)=hh0 TEMPthe temperature at which you are operating=300
The CONVERT_TO_FES action with label ff0 calculates the following quantities:
 Quantity   
 Description  
ff0.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)=ff0 FILE the file on which to write the grid=fes_d0.dat
DUMPGRIDOutput 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)=hh0 FILE the file on which to write the grid=pop_d0.dat STRIDE the frequency with which the grid should be output to the file=878


HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
  ARGthe quantities that are being used to construct the histogram=ang0
  GRID_MIN the lower bounds for the grid=-pi   GRID_MAX the upper bounds for the grid=pi   GRID_BINthe number of bins for the grid=100
  BANDWIDTHthe bandwidths for kernel density esimtation=0.1
  LABELa label for the action so that its output can be referenced in the input to other actions=hh12
... HISTOGRAM

The HISTOGRAM action with label hh12 calculates the following quantities:
 Quantity   
 Description  
hh12.value
the estimate of the histogram as a function of the argument that was obtainedff12: 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)=hh12 TEMPthe temperature at which you are operating=300
The CONVERT_TO_FES action with label ff12 calculates the following quantities:
 Quantity   
 Description  
ff12.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)=ff12 FILE the file on which to write the grid=fes_ang0.dat STRIDE the frequency with which the grid should be output to the file=800

HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
  ARGthe quantities that are being used to construct the histogram=d0,ang0
  GRID_MIN the lower bounds for the grid=0.2,-pi   GRID_MAX the upper bounds for the grid=1.2,pi   GRID_BINthe number of bins for the grid=100,100
  BANDWIDTHthe bandwidths for kernel density esimtation=0.01,0.1
  LABELa label for the action so that its output can be referenced in the input to other actions=hh13
... HISTOGRAM

The HISTOGRAM action with label hh13 calculates the following quantities:
 Quantity   
 Description  
hh13.value
the estimate of the histogram as a function of the argument that was obtainedff13: 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)=hh13 TEMPthe temperature at which you are operating=300
The CONVERT_TO_FES action with label ff13 calculates the following quantities:
 Quantity   
 Description  
ff13.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)=ff13 FILE the file on which to write the grid=fes_d0ang0.dat STRIDE the frequency with which the grid should be output to the file=800


PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=*   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 #UPDATE_FROM=500