LAMMPS triclinic simulation box for rigid-body MD simulations

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1

Dear all,

I need to simulate rigid-body MD simulations (for lipid layers). Is there any possibility for me in LAMMPS to perform these simulations using a triclinic simulation box?

[While exploring LAMMPS documentation and code I noticed that 2 barostats are available for pressure control:
Berendsen barostat that works with orthogonal simulation box only but it is used for rigid-body MD simulations and Nose-Hoover barostat that works also with triclinic simulation box but is used for atomistic simulations.]

Thank you in advance for your answer,
Ardita

2

yes, fix rigid should work with triclinic boxes. The fix rigid
doc page has a discussion of NPT options to use
with fix rigid.

Steve

3

Dear Steve Plimpton,

thank you for your prompt answer. While exploring the “fix rigid” doc page in http://lammps.sandia.gov/doc/fix_rigid.html I ran into the following statement:
"NOTE: Currently the rigid/npt and rigid/nph styles do not support triclinic (non-orthongonal) boxes. "

4

ok - so what is your question?

Steve

5

Dear Steve,

thank you for your prompt help and availability.

I am currently using the Elba-force field for the coarse-grain simulation of lipid and water particles to simulate lipid layers.

In particular the input scripts for LAMMPS that I am using include a hybrid atom style and use angle, dipole and sphere styles and pair_style dipole/sf 12
bond_style harmonic, angle_style hybrid cosine/squared dipole.

To control pressure and temperature I am using a Berendsen barostat and Langevin thermostat respectively. The Berendsen barostat does not perform any integration so I use the fix nve/sphere update dipole integrator.

The Berendsen barostat works with orthogonal simulation box only. Hence, I was wondering whether there is a way to have a triclinic simulation box for the same styles.

In this case, if I change the barostat from Berendsen to Nose-Hoover (using fix nph) mantaining a Langevin thermostat, I have to take into account that the Nose-Hoover barostat performs time integration as well so I should not include fix nve/sphere update dipole integrator anymore. I am not sure if this time integration (fix nph) takes into account the rotational motion of the coarse grain particles.

Thank you again,
Ardita