PLUMED-NEST

Project ID: plumID:23.007
Source: plumed-nest/nrpe3/cn.dat
Originally used with PLUMED version: 2.4.2
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

r1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=13,22 #res 1 and 10 agg in trial 1
The COM action with label r1 calculates somethingr2: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=41,50
The COM action with label r2 calculates somethingr3: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=63,72

The COM action with label r3 calculates somethingc: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r1,r1,r2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r2,r3,r3 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10 PAIR Pair only 1st element of the 1st group with 1st element in the second, etc

The COORDINATION action with label c calculates the following quantities:
 Quantity   
 Description  
c.value
the value of the coordinationc1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r2 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c1 calculates the following quantities:
 Quantity   
 Description  
c1.value
the value of the coordinationc2: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r3 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c2 calculates the following quantities:
 Quantity   
 Description  
c2.value
the value of the coordinationc3: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=r2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=r3 R_0The r_0 parameter of the switching function=0.5 NN The n parameter of the switching function =8 MM The m parameter of the switching function; 0 implies 2*NN=12  NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.75 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=10
The COORDINATION action with label c3 calculates the following quantities:
 Quantity   
 Description  
c3.value
the value of the coordination