[lammps-users] Fixing the bond lengths in n-alkane

Dear All,

I would like to simulate an n-alkane (C6H14). I have created a simple program to generate molecular positions by treating the CH3 and CH2 as pseudo-atoms. The format of the data file is as required by Lammps and is called by the read_data command. I would like to ask if there is a command or method to keep the bond lengths fixed. The fix_shake command can constrain CH2 or CH3 groups but not all the C-C backbone bonds for a long polymer chain. Could you please let me know if anyone has a suggestion ?(or if someone has simulated n-alkanes before).

Nicholas Epiphaniou

MPhill/PhD student

Aerospace Sciences
Fluid Mechanics and Computational Science Group
Cranfield University
School of Engineering
Cranfield,Bedfordshire MK43 0AL
UK
Email: [email protected]…51… <mailto:[email protected]…51…>

Sorry, this isn't something LAMMPS can do, at least in parallel.
You could write your own fix shake to do it in serial, using
the traditional SHAKE algorithm, but I don't know a simple
scalable way to do it in parallel. You might look at other
MD codes, like DL-POLY or GROMACS, which since they have
replicated data versions, may be able to do it,

Steve

You could use fix POEMS to do this type of simulation. You’d make rigid bodies of each pair of bonded atoms, but I don’t think it would run very fast. We’ve done n-alkanes in this way. Rudranarayan Mukherjee from RPI might also be able to help or comment on this. -Paul