PLUMED-NEST

Project ID: plumID:24.035
Source: examples/2_subsampling_formate/a_input/plumed.dat
Originally used with PLUMED version: 2.9
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
The UNITS action with label  calculates somethingCu: 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=5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52
The GROUP action with label Cu calculates somethingO: 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=2,3
The GROUP action with label O calculates somethingC: 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
The GROUP action with label C calculates somethingH: 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=4
The GROUP action with label H calculates somethingcoord_Cu-O: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=Cu GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=O R_0The r_0 parameter of the switching function=2.97 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12
The COORDINATION action with label coord_Cu-O calculates the following quantities:
 Quantity   
 Description  
coord_Cu-O.value
the value of the coordinationcoord_Cu-C: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=Cu GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=C R_0The r_0 parameter of the switching function=3.12 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12
The COORDINATION action with label coord_Cu-C calculates the following quantities:
 Quantity   
 Description  
coord_Cu-C.value
the value of the coordinationcoord_Cu-H: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=Cu GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=H R_0The r_0 parameter of the switching function=2.45 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12
The COORDINATION action with label coord_Cu-H calculates the following quantities:
 Quantity   
 Description  
coord_Cu-H.value
the value of the coordinationcoord_O-C: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=O GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=C R_0The r_0 parameter of the switching function=2.13 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12
The COORDINATION action with label coord_O-C calculates the following quantities:
 Quantity   
 Description  
coord_O-C.value
the value of the coordinationcoord_O-H: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=O GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=H R_0The r_0 parameter of the switching function=1.46 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12
The COORDINATION action with label coord_O-H calculates the following quantities:
 Quantity   
 Description  
coord_O-H.value
the value of the coordinationcoord_C-H: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=C GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=H R_0The r_0 parameter of the switching function=1.60 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12
The COORDINATION action with label coord_C-H calculates the following quantities:
 Quantity   
 Description  
coord_C-H.value
the value of the coordinationdist_O-O: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,3
The DISTANCE action with label dist_O-O calculates the following quantities:
 Quantity   
 Description  
dist_O-O.value
the DISTANCE between this pair of atomsPRINTPrint 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