Gap in my system

Dear All users,

I want to add a gap between my surface and molecular environment. Are ther any options in vmd

for performing this? Or Can I add a gap wherever in my simulation box? I want to omit the

interactions between them, my surface(crystal) and molecules.

In my view one probable approach can be this but I am not sure about it,

My system should be pbc in all directions. I want to add this gap below the end of my

structure therefore when I write the after that I will increase the box size in direction

x while there are not any atoms from the bottom of my system to my structure.

Is it possible? or Will Lammps perform it what I want to reach?

Hi Ali,

While I did not understand your question fully. Here is one option. If you have a periodic box, and you want to introduce the gap of XX angstroms

After reading the data file.

  1. Use change box command to increase the box by XX Angs (or larger if you want to have the gap on both sides of the crystal surface) in specified direction

  2. define a group of molecules, i.e., everything but crystal

  3. Use displace_atoms commands to move that group by XX angs in the same direction.

  4. run 0, save the restart file and convert it to data for visualization verification.


Dear Vikas,

Thank you very much for your reply.

I think it is crystal clear because of my periodic boundary condition having a surface at the bottom of my structure

some of my particles can have interaction with my surface. Your solution nearly is similar to mine.

Dear Vikas,

Your method was right and my method was wrong. But I have a question when I passed by step 3 but at step 4 I have

problem with the tool for conversion my restart file to data file while this conversion is necessary to me. I have used hybrid pair style and I got

this error when I run the cpp code for conversion.

Are you using the version of restart2data.cpp which is compatible with the lammps executable. If the lammps version and restart2data version are too far off, you sometimes get this error. Try installing the latest version of lammps, test your code and then use the restart2data.cpp file which is in /tools/ folder of that particular lammps tree.

If that does not solve the problem, hybrid style could be a issue, but it is hard to say at this point.