PLUMED-NEST

Click on the labels of the actions for more information on what each action computes

# vim: ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
#RESTART
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=0.001  #Amstroeng, kJ/mol, fs

The UNITS action with label  calculates somethingLi: 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=1-1000:1
The GROUP action with label Li 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=1001
The GROUP action with label N 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=1002,1003,1004

The GROUP action with label H calculates somethingdnh: DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=N GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=H MAXcalculate the maximum value={BETA=0.05} MINcalculate the minimum value={BETA=20.0}

The DISTANCES action with label dnh calculates the following quantities:
 Quantity   
 Description  
dnh.min
the minimum colvar
dnh.max
the maximum colvar
dnh.value
the DISTANCES between the each pair of atoms that were specifiedc1: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=N SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=H R_0The r_0 parameter of the switching function=2.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12 MAXcalculate the maximum value={BETA=0.05} MINcalculate the minimum value={BETA=20.0}

The COORDINATIONNUMBER action with label c1 calculates the following quantities:
 Quantity   
 Description  
c1.min
the minimum colvar
c1.max
the maximum colvar
c1.value
the coordination numbers of the specified atomscnh1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=N GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=1002 R_0The r_0 parameter of the switching function=2.0
The COORDINATION action with label cnh1 calculates the following quantities:
 Quantity   
 Description  
cnh1.value
the value of the coordinationcnh2: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=N GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=1003 R_0The r_0 parameter of the switching function=2.0 
The COORDINATION action with label cnh2 calculates the following quantities:
 Quantity   
 Description  
cnh2.value
the value of the coordinationcnh3: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=N GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=1004 R_0The r_0 parameter of the switching function=2.0 

The COORDINATION action with label cnh3 calculates the following quantities:
 Quantity   
 Description  
cnh3.value
the value of the coordinationctot: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cnh1,cnh2,cnh3 FUNCthe function you wish to evaluate=x+y+z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

The CUSTOM action with label ctot calculates the following quantities:
 Quantity   
 Description  
ctot.value
an arbitrary functionPRINTPrint 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=50 FILEthe name of the file on which to output these quantities=COLVAR
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