I am using fix shake command for CH2 group, cyclohexane (CH2)6. But I got the error message
"Shake clusters are connected"
I checked this means "A single cluster specified by the fix shake command must have a single
central atom with up to 3 other atoms bonded to it". However, in this specific ring structure molecule, how can be only one central atom? Can anyone tell me how should I use this command for cyclohexane?
And another question, is there any command in LAMMPS can exclude the intramolecular pair-wise interactions? I only want angle_style and dihedral_style potentials are used within one molecule, and the bond length is fixed.
Your help would be most appreciated.
-- Mechanical and Aerospace Engineering Department School of Engineering and Applied Science The George Washington University