[lammps-users] Bead-spring model polymer: movement of center of mass

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1

Dear Lammps users:

I have been running a system with neutral polymer (simple LJ-bead spring model) with and without solvent molecules. I dump in “DCD” format and when I visualize the system, I find the following:

  1. The polymer without any solvent molecules stays at the center of the box, and doesn’t diffuse much

  2. With the addition of even a single solvent molecule, the polymer diffuses a lot within the box.

  3. in Case 2, even when the interaction between polymer and solvent is completely turned off, the polymer diffuses by the mere presence of solvent molecules.

  4. Measuring radius of gyration as a function of N monomers, does a show (albeit small) difference with and with out solvent molecules.

Are there any "fix"es that I need to use?

-Thanks
Satya

My MD-input file:

2

Hi, Satya. This doesn’t make sense, on several levels. A couple questions to think about:

A) You create velocities without zeroing momentum. The polymer should have a ballistic motion, not merely a diffusive one. And the center of mass should diffuse.

B) Are you really sure you’re measuring “diffusion” and not deterministic motion (including that produced by the random seed used to create the velocities)?

C) Have you tested your point (4) for statistical significance?

Best,
Rob

3

Hi Rob,

What you mentioned in (A) is what is worrying me. What I see in the system (as I mentioned in my query) is that when no solute molecules are added, the polymer molecule collapses (from an initial extended state) to a condensed phase but essentially stays at the center of the box and does not undergo any motion.

The polymer is neutral and the interaction between polymer and solute molecules is attractive. What is not obvious to me is why is the polymer does not move around the box when no solute molecules were added, but does so (behave properly) when very few molecules of solvent (even 1) are added.

-Thanks
Satya

4

Well, an interacting solute molecule is one thing, but you seemed to say in point (3) of your original email that this occurs even if the interaction is turned off. And you haven’t addressed the question of what type of motion you’re really seeing.

Best,
Rob