PLUMED-NEST

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 somethingCo: 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=2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,58,60,62,64,66,68,70,72,74,76,78,80,82,84,86,88,90,92,94,96,98,100,102,104,106,108,110,112,114,116,118,120,122,124,126,128,130,132,134,136,138,140,142,144
The GROUP action with label Co calculates somethingFe: 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=1,3,5,7,9,11,13,15,17,19,21,23,25,27,29,31,33,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,79,81,83,85,87,89,91,93,95,97,99,101,103,105,107,109,111,113,115,117,119,121,123,125,127,129,131,133,135,137,139,141,143
The GROUP action with label Fe calculates somethingN: 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=145,146
The GROUP action with label N calculates somethingcoord_Co-Fe: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=Co GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=Fe R_0The r_0 parameter of the switching function=3.87 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_Co-Fe calculates the following quantities:
 Quantity   
 Description  
coord_Co-Fe.value
the value of the coordinationcoord_Co-N: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=Co GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=N R_0The r_0 parameter of the switching function=2.96 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_Co-N calculates the following quantities:
 Quantity   
 Description  
coord_Co-N.value
the value of the coordinationcoord_Fe-N: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=Fe GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=N R_0The r_0 parameter of the switching function=3.05 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_Fe-N calculates the following quantities:
 Quantity   
 Description  
coord_Fe-N.value
the value of the coordinationdist_N-N: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=145,146
The DISTANCE action with label dist_N-N calculates the following quantities:
 Quantity   
 Description  
dist_N-N.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