Dear lammps-users:
I constucted a system about hexadecane，when I use fix shake command,lammps shows ERROR: shake clusters are clusted.and I have read the manual again,and found that LAMMPS allows for the following kinds of clusters to be constrained: one central atom bonded to 1 or 2 or 3 atoms,such as water，CH2 or CH3 groups.I’M confused how to cosntrain CH2 or CH3 groups in hexadecane.
Eagerly waiting for the reply, and thank you very much!
Sincerely yours
Sneaker Bai
Dear lammps-users:
I constucted a system about hexadecane，when I use fix shake
command,lammps shows ERROR: shake clusters are clusted.and I have read the
manual again,and found that LAMMPS allows for the following kinds of
clusters to be constrained: one central atom bonded to 1 or 2 or 3
atoms,such as water，CH2 or CH3 groups.I'M confused how to cosntrain CH2 or
CH3 groups in hexadecane.
for a more specific and detailed answer, it is necessary to know the
exact fix shake command you are using.
also, your statement "constrain CH2 or CH3 groups" is ambiguous. as
should be obvious from the limitations of fix shake described in the
documentation, for your molecule, you can only constrain the C-H
bonds, not H-C-H angles or C-C-H angles, as those would lead to
"connected clusters".
axel.