Multiple groups of atoms of a molecule need to be identified as rigid/small

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1

Hello Lammps Users,

I am new to lammps. I would like to apply the gcmc fix on a molecule. I have input the molecule using the molecule command. The molecule’s structure consists of 2 domains which are linked by a chain. So I would like the two domains to act as rigid bodies. Inorder to do so I have to apply the rigid/small fix. But the rigid/small fix groups the whole molecule and considers the whole molecule as one rigid body since they all have the same molecule template ID. Could you please guide on me how can I make the two domains of the same molecule inputed using molecule command be identified as rigid/small

Thanking you in advance.

Regards,
Birva Patel

2

Hello Lammps Users,

I am new to lammps. I would like to apply the gcmc fix on a molecule. I
have input the molecule using the molecule command. The molecule’s
structure consists of 2 domains which are linked by a chain. So I would
like the two domains to act as rigid bodies. Inorder to do so I have to
apply the rigid/small fix. But the rigid/small fix groups the whole
molecule and considers the whole molecule as one rigid body since they all
have the same molecule template ID. Could you please guide on me how can I
make the two domains of the same molecule inputed using molecule command be
identified as rigid/small

​this is currently not possible, and i don't see an easy way to implement
this. i would also be doubtful, that fix gcmc as implemented in LAMMPS is
meaningful on such a "large" molecule. ​

​axel.​

3

Dear Axel,

I would like to perform Monte Carlo simulation on this molecule using lammps. Could you tell me on how could I perform MC simulation which will facilitate rigid body simulation as well using lammps.

Thanking you,
Birva Patel

4

LAMMPS is an MD code and not an MC code. Just look at the documentation and see. If you want to turn it into an MC code, you will have to do a lot of C++ programming.

Axel.

5

I only comment on the fix rigid part, not the MC part.

You can define rigid bodies which are connected by bonds.

You just need to use molecule IDs in your input data file

which are distinct for different subsets of the actual molecules.

LAMMPS only uses molecule IDs for a few things like fix rigid,

so you can define them however you wish.

Steve