a question in fix rigid

Hi all,

I am trying to simulate a Carbon Structure (CNT and/or Graphene) and my initial try is to use a rigid formulation. For that reason I used the following pair coeff command:

pair_coeff      * * lj/cut 0.086 3.4  0.0  # epsilon sigma cut-off radius 
I am trying now to change the 0.0 (just to experiment with in a MD framework) with let's say 1.0 or something. From this time when I am trying to run a simulation I am getting NaN and Infs. Why is this happening? I know that it is caused due to the rigid but why it is affected ?

jim  

Hi all,

I am trying to simulate a Carbon Structure (CNT and/or Graphene) and my
initial try is to use a rigid formulation. For that reason I used the
following pair coeff command:

pair_coeff * * lj/cut 0.086 3.4 0.0 # epsilon sigma cut-off radius

I am trying now to change the 0.0 (just to experiment with in a MD
framework) with let's say 1.0 or something. From this time when I am trying
to run a simulation I am getting NaN and Infs. Why is this happening? I know
that it is caused due to the rigid but why it is affected ?

what makes you think that this is cause by fix rigid?

from what you describe, i would suspect you have a
bad configuration. with a cutoff of 0 you have turned
off the interaction so you won't see any bad contacts,
but with a finite cutoff you do see them and they can
lead to NaNs and Infs.

axel.

what makes you think that this is cause by fix rigid?

It is just a guess. I don’t think it is a bad configuration since when I am using a non-rigid structure (bonds angles etc…) it works . i tried the same thing in a CNT created by VMD (to eliminate the possibility of the bad configuration) and still the same problem.

Jim

what makes you think that this is cause by fix rigid?

It is just a guess. I don't think it is a bad configuration since when I am
using a non-rigid structure (bonds angles etc...) it works . i tried the

what is "it" in this context?

same thing in a CNT created by VMD (to eliminate the possibility of the bad
configuration) and still the same problem.

you can still have bad contacts through bad choice
of the simulation box.

however, it is useless to speculate, when you can just show us.

please provide a simple input example that reproduces the problem,
but you believe it should work and the counter example w/o fix rigid
that does work. then it becomes a simple matter of comparing and
debugging instead of speculating and guessing.

thanks,
     axel.