Hello,
I am trying to simulate the movement of a nanoparticle within a 3D periodic box filled with simple Lennard Jones atoms.
the nanoparticle is constructed by 10~20 atoms and are held together by applying the “fix rigid” with identical mass to Lennard Jones atoms.
here is the portion of the script I use:
units lj
dimension 3
boundary p p p
.
.
.
group fluid type 1
group NP type 2 3 4
.
.
.
fix 1 fluid nvt temp 1.1 1.1 1.0
fix 2 NP rigid single
the group name “NP” is for the nanoparticle which is fixed via “fix rigid single” and “fluid” are the simple lennard Jones atoms, filling the box, which are integrated using nose hoover thermostat.
The size of the simulation box is around ten times bigger than the NP diameter to reduce the periodic BC effects.
However, when I compute the center of mass for fluid atoms there is a very massive drift.
I would like the nanoparticle to move completely free on its own from it`s interaction with the surrounding fluid atoms.
I would appreciate if you could give me some hint where this massive drifting could come from.
Thanks in advance,
Hello,
I am trying to simulate the movement of a nanoparticle within a 3D
periodic box filled with simple Lennard Jones atoms.
the nanoparticle is constructed by 10~20 atoms and are held together by
applying the "fix rigid" with identical mass to Lennard Jones atoms.
here is the portion of the script I use:
units lj
dimension 3
boundary p p p
.
.
.
group fluid type 1
group NP type 2 3 4
.
.
.
fix 1 fluid nvt temp 1.1 1.1 1.0
fix 2 NP rigid single
the group name "NP" is for the nanoparticle which is fixed via "fix rigid
single" and "fluid" are the simple lennard Jones atoms, filling the box,
which are integrated using nose hoover thermostat.
The size of the simulation box is around ten times bigger than the NP
diameter to reduce the periodic BC effects.
However, when I compute the center of mass for fluid atoms there is a very
massive drift.
I would like the nanoparticle to move completely free on its own from it`s
interaction with the surrounding fluid atoms.
I would appreciate if you could give me some hint where this massive
drifting could come from.
have a look out for "flying icecube syndrome" in the mailing list archives.
that would be the most likely explanation. there is too little information
to say more.
axel.
However, when I compute the center of mass for fluid atoms there is a very
massive drift.
I would like the nanoparticle to move completely free on its own from it`s
interaction with the surrounding fluid atoms.
I'm not sure what you mean by this. If you want the NP to just move
without "feeling" the solvent, then don't define an interaction between them,
or just use fix move on the NP to move it in a prescribed manner. But if you
do that the fluid (which does feel the NP) will certainly be affected by its
motion. It's like an external field on the solvent so the COM of the fluid
will certainly change.
Steve
Steve,
Thanks for your reply. I do want the NP to feel the solvent but I do not want to introduce any artificial external effects like thermostat on it. therefore, only the kicks from the surrounding atoms translate and rotates the NP.
I am aware of the influence of the NP on the fluid Center of Mass but since the mass of the NP is identical to the solvent atoms I am not expecting a drastic drift in fluid COM.
Thanks,
However, when I compute the center of mass for fluid atoms there is a very
massive drift.
I would like the nanoparticle to move completely free on its own from it`s
interaction with the surrounding fluid atoms.
I’m not sure what you mean by this. If you want the NP to just move
without “feeling” the solvent, then don’t define an interaction between them,
or just use fix move on the NP to move it in a prescribed manner. But if you
do that the fluid (which does feel the NP) will certainly be affected by its
motion. It’s like an external field on the solvent so the COM of the fluid
will certainly change.
Steve