[lammps-users] Can shake in LAMMPS constrain all the bond length in hexane molecule?

Hi, all

I would like to simulate hexane molecules with C atoms attached one by one and have those C-C bonds fixed using “fix shake”.
But I found in the manual about fix shake, “LAMMPS allows for the following kinds of clusters to be constrained: one central atom bonded to 1 or 2 or 3 atoms, or one central atom bonded to 2 others and the angle between the 3 atoms also constrained. This means water molecules of CH2 or CH3 groups may be constrained, but not all the C-C backbone bonds of a long polymer chain.” When performing the simulation I get an error said “Shake clusters are connected”. Since methods described in literatures said all C-C bond length can be constrained, I want to know whether shake method incorprated in LAMMPS can constrain all the C-C bonds in such hexane chains or there are other choices to get what I intend to do.

No, you can't shake all the C-C bonds in hexane. That's what the
doc page is telling you. You could try fix rigid for just the C atoms
in each molecule.