Deformation of system with rigid and non rigid bodies

Dear all,

I have to perform uni-axial deformation procedure to my polymer system which has rigid and non rigid atoms. There are 6660 number of atoms, out of which 800 atoms are rigid atoms. The rigid atoms are allowed to move only in a group. Below is the procedure

  1. Minimization
  2. NVT at 300 K
  3. NPT at 300 K

I am using the following script.

include “crystal_n.txt” # contains ids of rigid atoms
group all id 1:6660
group crystal union crys1
group amorphous subtract all crystal # contains ids of non-rigid atoms

neigh_modify exclude molecule crystal

Fix deform applies to the simulation box.
Typically you want all atoms in the box (rigid
or non-rigid) to be deformed as well. The fix
deform command has options to move
the atoms with the deforming box or not,
and which group of atoms to apply itself to.
So it’s up to you and your model how to use it.