Constrain Z positions of atoms in rigid graphene

Hello LAMMPS users, I am using windows 30 july 2021. I want to pull a graphene out of epoxy. I am interested in finding change in potential energy with respect to pull-out distance in x direction. Accordingly, boundary conditions are m p m for x,y and z direction.

Before pulling out graphene, I equilibrated structure at 0.01 K.

Top layer of epoxy in Z direction 10 A is kept fixed out of 55A epoxy by not time integrating and named as group polymerfix. Rest of epoxy molecules is assigned group as polymermov.

In case of a graphene, I have assigned a group named as pullatoms for first row of a graphene and kept stationary by not time integrating, and rest graphene atoms are assigned to a group named as rigidgraphene. I do not want movement of graphene atoms in z direction. Therefore, I used command velocity and setforce.

Command used as

velocity rigidgraphene set NULL NULL 0.0

fix fzrigidgraphene rigidgraphene setforce NULL NULL 0.0

fix 2 polymermov nvt temp 1E-8 1E-8 100

fix 3 rigidgraphene rigid/nvt single temp 0.1 0.1 100

I observed in trajectory that atoms of graphene in z direction are in the same direction as z positions are in initial data file. Z positions of atoms only varied by 10.34 to 10.36 A.

But when I used same script for functionalized graphene. I am observing up and down movement in functionalized graphene as shown in Fig. below. How can I make rigidgraphene such as its Z positions doe not change.

Thank you,

I suspect you would be better off using fix aveforce. But if you want your functionalized graphene to not move, why not … not integrate it at all? (That is, do you want it rigid, or immobile?)

1 Like


A solution that is common to free energy method (which I assume you are doing?) is to fix the (average) position of the graphene using an additional harmonic potential using fix spring.

Of course there is also always the possibility to just exclude the graphene from any fix that update the atom positions, and in that case it is not gonna move in any directions.


1 Like

Thank you, @srtee and @simongravelle for your suggestions. Not integrating the atoms can be a good option here.