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

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1

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: n.epiphaniou@…51… <mailto:n.epiphaniou@…51…>

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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

3

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