[lammps-users] Fixing the bond length in alkanes

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1

I am simulating alkanes (currently dodecane) using LAMMPS.

I am treating by molecule as being made up of CH3 and CH2 groups, and am using the OPLS force field to define my bonds, angles, dihedrals.

Is it possible to keep the bond length fixed in LAMMPS. I have seen the fix_shake command, but this says it can only be used for very small molecules and cannot be used for a hydrocarbon backbone.

Thanks,

Michael Doig
PhD Student
University of Edinburgh

2

Nope, LAMMPS doesn't allow you to do SHAKE
on a long, linked set of bonds, like a backbone. The
issue is that it is not a very parallel operation to apply
that kind of constraint on a chain that may span many
processors. But you can always use a flexible alkane
(flexible along the backbone), and use rRESPA for
example to extend the timescale to the same timestep
SHAKE would use.

Steve