Overlap in Starting Configuration of Adsorbate in Rigid Framework

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1

Hello,

I’m trying to run some simulations of methane in a rigid MOF-5 framework. I use moltemplate to generate the starting configuration, but the problem is that there’s overlap between the methane atoms and the MOF-5 atoms, which blows the methane atoms out of the box.

Currently, I’m solving this problem by running a separate Monte Carlo simulation of methane in MOF-5, and I use the results of that simulation as my starting coordinates.

However, I feel like there should be a more elegant way to solve this problem. Unfortunately I can’t relax the whole box, because I don’t want the MOF-5 atoms to change position. Is there a good LAMMPS way to solve this?

Thanks in advance,

2

Hello,

I'm trying to run some simulations of methane in a rigid MOF-5 framework. I
use moltemplate to generate the starting configuration, but the problem is
that there's overlap between the methane atoms and the MOF-5 atoms, which
blows the methane atoms out of the box.

Currently, I'm solving this problem by running a separate Monte Carlo
simulation of methane in MOF-5, and I use the results of that simulation as
my starting coordinates.

However, I feel like there should be a more elegant way to solve this
problem. Unfortunately I can't relax the whole box, because I don't want the
MOF-5 atoms to change position. Is there a good LAMMPS way to solve this?

you could use a soft (core) potential in combination with fix adapt to
"unoverlap" atoms. check out the micelle example.

axel.

3

You can also do a relaxation (minimize command) of
just the non-MOF atoms. See the fix setforce
command (set forces to 0.0) and its doc page
about how it operates in minimize mode.

Steve