question of a rigid particle

Hello,

I have a problem of simulating a system with a rectangular rigid particle:
the rigid particle collapses in a different way depending on “bond_coeff” (e.g., k=10, or 100).
(please see attached pictures.)

The collapse happens even if I use “boundary p p f”, “fix rigid/nvt”, “fix nve”, or “fix npt”.

Herein, I am attaching my input script below.
Would anyone help me?

Thank you.

c2.JPG

c1.JPG

Hello,
I have a problem of simulating a system with a rectangular rigid particle:
the rigid particle collapses in a different way depending on "bond_coeff"
(e.g., k=10, or 100).
(please see attached pictures.)
The collapse happens even if I use "boundary p p f", "fix rigid/nvt", "fix
nve", or "fix npt".

how do you expect that particle to remain intact,
if you do not use fix rigid or fix rigid/nvt ?

Herein, I am attaching my input script below.

that script _cannot_ work.

try posting one that uses any of the "rigid" fixes
and explain where that one fails.

axel.

Thank you.

If I set a strong harmonic bond and a pseudo harmonic angle, those particles should be remained intact, right?
As I mentioned in the previous email, “fix rigid/nvt” does not work either. (same collapse happens.)
Please try with attached in and data files.

Thank you.

rigid.data (10.3 KB)

rigid_1.in (886 Bytes)

Thank you.
If I set a strong harmonic bond and a pseudo harmonic angle, those particles
should be remained intact, right?

mostly. it will bend and twist.

As I mentioned in the previous email, "fix rigid/nvt" does not work either.
(same collapse happens.)

there is no collapse. just look at the trajectory.
your "rigid" particle is just crossing a periodic boundary.

do you want those "rigid" atoms to move?
or do you want them just to be fixed in space?
it looks to me almost as you want the latter.
and that is easier achieved by simply not
including them into the integration fix.

something like this:

read_data rigid.data
group rigid type 2
group mobile subtract all rigid

and then:

fix 1 mobile nvt temp 1.0 1.0 5.0

but your input has other issues, too.

you cannot have a "naked" coulomb.
those atoms will collapse and crash the simulation.
the whole model looks very strange.

axel.

axel.

Thank you!

Some atoms’ coordinations were far from their origin, so I thought it was “collapse”.
After I manually rearranged those atoms in a periodic boundary with better-looking, I found you’re right.
Do you know any good software of rearranging atoms that crossed a periodic boundary?

By the way,
How can I handle a charged atom instead of using “naked” coulomb?

Thanks again.

Thank you!
Some atoms' coordinations were far from their origin, so I thought it was
"collapse".
After I manually rearranged those atoms in a periodic boundary with
better-looking, I found you're right.

Do you know any good software of rearranging atoms that crossed a periodic
boundary?

just write atom style dump instead of .xyz (so that you have box information)
and then you can use VMD with pbctools (load the trajectory, go to the first
frame, then do pbc unwrap -all)

By the way,
How can I handle a charged atom instead of using "naked" coulomb?

have you looked at what is done in typical force fields?

you have to have some idea of what you want to model and
what is a good set of potentials and parameters for that.

there is no generic answer for this.

axel.