the issue of the simulation of rigid methane molecules in LAMMPS

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1

Hi, ALL

I am trying to run simulations of a system involving rigid methane molecules. However,
it seems that SHAKE in LAMMPS can not handle methane because the carbon is connected
to 4 hydrogen atoms. In the manual, it mentions that

“LAMMPS allows for the following kinds of clusters to be constrained: one central atom
bonded to 1 or 2 or 3 atoms, or one central atom bonded to 2 others and the angle between
the 3 atoms also constrained.”

BTW, to ensure the rigidity of the methane molecule, I defined 9 distances for methane, i.e.
4 C-H bond, and 5 H-H bond.

Is there anyway to circumvent this issue ? Thanks.

Guozhen

2

Hi, ALL

  I am trying to run simulations of a system involving rigid methane

molecules. However,
it seems that SHAKE in LAMMPS can not handle methane because the carbon is
connected
to 4 hydrogen atoms. In the manual, it mentions that

"LAMMPS allows for the following kinds of clusters to be constrained: one
central atom
bonded to 1 or 2 or 3 atoms, or one central atom bonded to 2 others and the
angle between
the 3 atoms also constrained."

 BTW, to ensure the rigidity of the methane molecule, I defined 9

distances for methane, i.e.
4 C-H bond, and 5 H-H bond.

Is there anyway to circumvent this issue ? Thanks\.

there are three options:

- implement a version of SHAKE that allows more complicated
  constraints (at the expense of parallel efficiency).

- use one of the "rigid" integrators instead,
  those will integrate the translational and
  rotational degrees of freedom separately.

- use a united atom model. that is often a
  reasonable approximation, since methane
  is almost spherical.

axel.

3

Hi, ALL

I am trying to run simulations of a system involving rigid methane
molecules. However,
it seems that SHAKE in LAMMPS can not handle methane because the carbon is
connected
to 4 hydrogen atoms. In the manual, it mentions that

“LAMMPS allows for the following kinds of clusters to be constrained: one
central atom
bonded to 1 or 2 or 3 atoms, or one central atom bonded to 2 others and the
angle between
the 3 atoms also constrained.”

BTW, to ensure the rigidity of the methane molecule, I defined 9
distances for methane, i.e.
4 C-H bond, and 5 H-H bond.

Is there anyway to circumvent this issue ? Thanks.

there are three options:

  • implement a version of SHAKE that allows more complicated
    constraints (at the expense of parallel efficiency).

  • use one of the “rigid” integrators instead,
    those will integrate the translational and
    rotational degrees of freedom separately.

How to use this option ? Thanks.

4

http://lammps.sandia.gov/doc/fix_rigid.html

make sure to start with a small enough timestep,
the integration of rotational d.o.f.s is more
more fragile than the integration of the c.o.m.

a.

5

Hi, ALL

I am trying to run simulations of a system involving rigid methane
molecules. However,
it seems that SHAKE in LAMMPS can not handle methane because the carbon
is
connected
to 4 hydrogen atoms. In the manual, it mentions that

“LAMMPS allows for the following kinds of clusters to be constrained:
one
central atom
bonded to 1 or 2 or 3 atoms, or one central atom bonded to 2 others and
the
angle between
the 3 atoms also constrained.”

BTW, to ensure the rigidity of the methane molecule, I defined 9
distances for methane, i.e.
4 C-H bond, and 5 H-H bond.

Is there anyway to circumvent this issue ? Thanks.

there are three options:

  • implement a version of SHAKE that allows more complicated
    constraints (at the expense of parallel efficiency).

  • use one of the “rigid” integrators instead,
    those will integrate the translational and
    rotational degrees of freedom separately.

How to use this option ? Thanks.

Thanks a lot !
One more question. What if I want to apply NPT to the system ?

6

then you have to program it. the paper describing
the rigid/nvt integrator also describes a rigid/npt
integrator, but it has not (yet) been implemented
and i am not sure if the author of rigid/nvt is still
working on it.

axel.

7

Is it reasonable to apply a very stiff bond potential on the methane molecule to mimic the rigidity ?

8

why not use the proper potentials for bonded interactions, then?

axel.