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).
Fluid Mechanics and Computational Science Group
School of Engineering
Cranfield,Bedfordshire MK43 0AL
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