PLUMED-NEST

Project ID: plumID:24.036
Source: PLIT/plumed_h1h2.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=1-166

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=14,32
The DISTANCE action with label d0 calculates the following quantities:
 Quantity   
 Description  
d0.value
the DISTANCE between this pair of atomsd1:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=14,35
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=8,27
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=9,11
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=9,23
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=21,23
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=35,40
The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Description  
d6.value
the DISTANCE between this pair of atomsddr0: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=14,62,63,17
The TORSION action with label ddr0 calculates the following quantities:
 Quantity   
 Description  
ddr0.value
the TORSION involving these atomsang0: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=1,62,65


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=50000
  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


HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
#UPDATE_FROM=50000
  ARGthe quantities that are being used to construct the histogram=d1
  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=hh1
... HISTOGRAM

The HISTOGRAM action with label hh1 calculates the following quantities:
 Quantity   
 Description  
hh1.value
the estimate of the histogram as a function of the argument that was obtainedff1: 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)=hh1 TEMPthe temperature at which you are operating=300
The CONVERT_TO_FES action with label ff1 calculates the following quantities:
 Quantity   
 Description  
ff1.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)=ff1 FILE the file on which to write the grid=fes_d1.dat

HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
#UPDATE_FROM=50000
  ARGthe quantities that are being used to construct the histogram=d2 
  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=hh2
... HISTOGRAM

The HISTOGRAM action with label hh2 calculates the following quantities:
 Quantity   
 Description  
hh2.value
the estimate of the histogram as a function of the argument that was obtainedff2: 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)=hh2 TEMPthe temperature at which you are operating=300
The CONVERT_TO_FES action with label ff2 calculates the following quantities:
 Quantity   
 Description  
ff2.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)=ff2 FILE the file on which to write the grid=fes_d2.dat

HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
#UPDATE_FROM=50000
  ARGthe quantities that are being used to construct the histogram=d3
  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=hh3
... HISTOGRAM

The HISTOGRAM action with label hh3 calculates the following quantities:
 Quantity   
 Description  
hh3.value
the estimate of the histogram as a function of the argument that was obtainedff3: 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)=hh3 TEMPthe temperature at which you are operating=300
The CONVERT_TO_FES action with label ff3 calculates the following quantities:
 Quantity   
 Description  
ff3.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)=ff3 FILE the file on which to write the grid=fes_d3.dat

HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
#UPDATE_FROM=50000
  ARGthe quantities that are being used to construct the histogram=d4
  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=hh4
... HISTOGRAM

The HISTOGRAM action with label hh4 calculates the following quantities:
 Quantity   
 Description  
hh4.value
the estimate of the histogram as a function of the argument that was obtainedff4: 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)=hh4 TEMPthe temperature at which you are operating=300
The CONVERT_TO_FES action with label ff4 calculates the following quantities:
 Quantity   
 Description  
ff4.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)=ff4 FILE the file on which to write the grid=fes_d4.dat

HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
#UPDATE_FROM=50000
  ARGthe quantities that are being used to construct the histogram=d5
  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=hh5
... HISTOGRAM

The HISTOGRAM action with label hh5 calculates the following quantities:
 Quantity   
 Description  
hh5.value
the estimate of the histogram as a function of the argument that was obtainedff5: 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)=hh5 TEMPthe temperature at which you are operating=300
The CONVERT_TO_FES action with label ff5 calculates the following quantities:
 Quantity   
 Description  
ff5.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)=ff5 FILE the file on which to write the grid=fes_d5.dat

HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
#UPDATE_FROM=50000
  ARGthe quantities that are being used to construct the histogram=d6
  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=hh6
... HISTOGRAM

The HISTOGRAM action with label hh6 calculates the following quantities:
 Quantity   
 Description  
hh6.value
the estimate of the histogram as a function of the argument that was obtainedff6: 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)=hh6 TEMPthe temperature at which you are operating=300
The CONVERT_TO_FES action with label ff6 calculates the following quantities:
 Quantity   
 Description  
ff6.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)=ff6 FILE the file on which to write the grid=fes_d6.dat


HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
#UPDATE_FROM=50000
  ARGthe quantities that are being used to construct the histogram=d0,d1
  GRID_MIN the lower bounds for the grid=0.2,0.2   GRID_MAX the upper bounds for the grid=1.2,1.2   GRID_BINthe number of bins for the grid=100,100
  BANDWIDTHthe bandwidths for kernel density esimtation=0.01,0.01
  LABELa label for the action so that its output can be referenced in the input to other actions=hh7
... HISTOGRAM

The HISTOGRAM action with label hh7 calculates the following quantities:
 Quantity   
 Description  
hh7.value
the estimate of the histogram as a function of the argument that was obtainedff7: 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)=hh7 TEMPthe temperature at which you are operating=300
The CONVERT_TO_FES action with label ff7 calculates the following quantities:
 Quantity   
 Description  
ff7.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)=ff7 FILE the file on which to write the grid=fes_d0d1.dat


HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
#UPDATE_FROM=50000
  ARGthe quantities that are being used to construct the histogram=d1,d2
  GRID_MIN the lower bounds for the grid=0.2,0.2   GRID_MAX the upper bounds for the grid=1.2,1.2   GRID_BINthe number of bins for the grid=100,100
  BANDWIDTHthe bandwidths for kernel density esimtation=0.01,0.01
  LABELa label for the action so that its output can be referenced in the input to other actions=hh8
... HISTOGRAM

The HISTOGRAM action with label hh8 calculates the following quantities:
 Quantity   
 Description  
hh8.value
the estimate of the histogram as a function of the argument that was obtainedff8: 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)=hh8 TEMPthe temperature at which you are operating=300
The CONVERT_TO_FES action with label ff8 calculates the following quantities:
 Quantity   
 Description  
ff8.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)=ff8 FILE the file on which to write the grid=fes_d1d2.dat

HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
#UPDATE_FROM=50000
  ARGthe quantities that are being used to construct the histogram=d2,d3
  GRID_MIN the lower bounds for the grid=0.2,0.2   GRID_MAX the upper bounds for the grid=1.2,1.2   GRID_BINthe number of bins for the grid=100,100
  BANDWIDTHthe bandwidths for kernel density esimtation=0.01,0.01
  LABELa label for the action so that its output can be referenced in the input to other actions=hh9
... HISTOGRAM

The HISTOGRAM action with label hh9 calculates the following quantities:
 Quantity   
 Description  
hh9.value
the estimate of the histogram as a function of the argument that was obtainedff9: 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)=hh9 TEMPthe temperature at which you are operating=300
The CONVERT_TO_FES action with label ff9 calculates the following quantities:
 Quantity   
 Description  
ff9.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)=ff9 FILE the file on which to write the grid=fes_d2d3.dat

HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
#UPDATE_FROM=50000
  ARGthe quantities that are being used to construct the histogram=d3,d4
  GRID_MIN the lower bounds for the grid=0.2,0.2   GRID_MAX the upper bounds for the grid=1.2,1.2   GRID_BINthe number of bins for the grid=100,100
  BANDWIDTHthe bandwidths for kernel density esimtation=0.01,0.01
  LABELa label for the action so that its output can be referenced in the input to other actions=hh10
... HISTOGRAM

The HISTOGRAM action with label hh10 calculates the following quantities:
 Quantity   
 Description  
hh10.value
the estimate of the histogram as a function of the argument that was obtainedff10: 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)=hh10 TEMPthe temperature at which you are operating=300
The CONVERT_TO_FES action with label ff10 calculates the following quantities:
 Quantity   
 Description  
ff10.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)=ff10 FILE the file on which to write the grid=fes_d3d4.dat

HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
#UPDATE_FROM=50000
  ARGthe quantities that are being used to construct the histogram=ddr0
  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=hh11
... HISTOGRAM

The HISTOGRAM action with label hh11 calculates the following quantities:
 Quantity   
 Description  
hh11.value
the estimate of the histogram as a function of the argument that was obtainedff11: 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)=hh11 TEMPthe temperature at which you are operating=300
The CONVERT_TO_FES action with label ff11 calculates the following quantities:
 Quantity   
 Description  
ff11.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)=ff11 FILE the file on which to write the grid=fes_ddr0.dat

HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
#UPDATE_FROM=50000
  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


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