PLUMED-NEST-TEST-SITE

Project ID: plumID:23.040
Source: plumed_analysis/pyrogallolarene/plumed_solvent.dat
Originally used with PLUMED version: 2.6
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

UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=1  #Amstroeng, hartree, fs

The UNITS action with label  calculates somethingWHOLEMOLECULESThis 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=1-76 ENTITY1the atoms that make up a molecule that you wish to align=77-152 ENTITY2the atoms that make up a molecule that you wish to align=153-228 ENTITY3the atoms that make up a molecule that you wish to align=229-304 ENTITY4the atoms that make up a molecule that you wish to align=305-380 ENTITY5the atoms that make up a molecule that you wish to align=381-456 

# Group definition
cal1The GROUP action with label cal1 calculates the following quantities:
 Quantity   
 Type   
 Description  
cal1
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-76
cal2The GROUP action with label cal2 calculates the following quantities:
 Quantity   
 Type   
 Description  
cal2
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=77-152
cal3The GROUP action with label cal3 calculates the following quantities:
 Quantity   
 Type   
 Description  
cal3
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=153-228
cal4The GROUP action with label cal4 calculates the following quantities:
 Quantity   
 Type   
 Description  
cal4
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=229-304
cal5The GROUP action with label cal5 calculates the following quantities:
 Quantity   
 Type   
 Description  
cal5
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=305-380
cal6The GROUP action with label cal6 calculates the following quantities:
 Quantity   
 Type   
 Description  
cal6
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=381-456

cl3_comThe GROUP action with label cl3_com calculates the following quantities:
 Quantity   
 Type   
 Description  
cl3_com
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index_files/com_cl3.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=CL3_COM

com1The CENTER_FAST action with label com1 calculates the following quantities:
 Quantity   
 Type   
 Description  
com1
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=cal1
com2The CENTER_FAST action with label com2 calculates the following quantities:
 Quantity   
 Type   
 Description  
com2
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=cal2
com3The CENTER_FAST action with label com3 calculates the following quantities:
 Quantity   
 Type   
 Description  
com3
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=cal3
com4The CENTER_FAST action with label com4 calculates the following quantities:
 Quantity   
 Type   
 Description  
com4
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=cal4
com5The CENTER_FAST action with label com5 calculates the following quantities:
 Quantity   
 Type   
 Description  
com5
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=cal5
com6The CENTER_FAST action with label com6 calculates the following quantities:
 Quantity   
 Type   
 Description  
com6
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=cal6

com_allThe CENTER_FAST action with label com_all calculates the following quantities:
 Quantity   
 Type   
 Description  
com_all
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=cal1,cal2,cal3,cal4,cal5,cal6

DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=inside_molThe DISTANCES action with label inside_mol calculates the following quantities:
 Quantity   
 Type   
 Description  
inside_mol
vector
the DISTANCES between the each pair of atoms that were specified
inside_mol_lessthan
scalar
the number of colvars that have a value less than a threshold
  GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=com_all 
  GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=cl3_com
  LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=6.5} 
... DISTANCES
# PLUMED interprets the command:
# DISTANCES ...
#   LABEL=inside_mol
#   GROUPA=com_all 
#   GROUPB=cl3_com
#   LESS_THAN={RATIONAL R_0=6.5} 
# ... DISTANCES
# as follows (Click the red comment above to revert to the short version of the input):
inside_molThe DISTANCE action with label inside_mol calculates the following quantities:
 Quantity   
 Type   
 Description  
inside_mol
vector
the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=com_all,458 ATOMS2the pair of atom that we are calculating the distance between=com_all,463 ATOMS3the pair of atom that we are calculating the distance between=com_all,468 ATOMS4the pair of atom that we are calculating the distance between=com_all,473 ATOMS5the pair of atom that we are calculating the distance between=com_all,478     # Action input conctinues with 2794 further ATOMSn keywords, 
inside_mol_ltThe LESS_THAN action with label inside_mol_lt calculates the following quantities:
 Quantity   
 Type   
 Description  
inside_mol_lt
vector
the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=inside_mol SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=6.5}
inside_mol_lessthanThe SUM action with label inside_mol_lessthan calculates the following quantities:
 Quantity   
 Type   
 Description  
inside_mol_lessthan
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=inside_mol_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=inside_mol.* FILEthe name of the file on which to output these quantities=solvent.dat STRIDE the frequency with which the quantities of interest should be output=1
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1