Project ID: plumID:21.015
Source: US/CBM5/plumed18.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=721-887the atoms that make up a molecule that you wish to align
a1:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=798-801 a2:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=803-807 a3:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=832-835 achi:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=1-720the group of atoms that you are calculating the Gyration Tensor for
p1:POSITIONCalculate the components of the position of an atom. More detailsATOM=a1the atom numberNOPBCp2:ignore the periodic boundary conditions when calculating distancesPOSITIONCalculate the components of the position of an atom. More detailsATOM=a2the atom numberNOPBCp3:ignore the periodic boundary conditions when calculating distancesPOSITIONCalculate the components of the position of an atom. More detailsATOM=a3the atom numberNOPBCpchi:ignore the periodic boundary conditions when calculating distancesPOSITIONCalculate the components of the position of an atom. More detailsATOM=achithe atom numberNOPBCignore the periodic boundary conditions when calculating distances
distx:MATHEVALAn alias to the ef CUSTOM function. More detailsARG=p1.x,p2.x,p3.x,pchi.xthe input to this functionVAR=a,b,c,ythe names to give each of the arguments in the functionFUNC=((y-a)^2+(y-b)^2+(y-c)^2)^0.5the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
restraint-bnd:RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More detailsARG=distxthe arguments on which the bias is actingKAPPA=100.0specifies that the restraint is harmonic and what the values of the force constants on each of the variables areAT=0.8the position of the restraintPrint quantities to a file. More detailsARG=distx,restraint-bnd.biasthe input for this action is the scalar output from one or more other actionsSTRIDE=5000the frequency with which the quantities of interest should be outputFILE=COLVAR18the name of the file on which to output these quantities