Methods of simulating shock propagation in protein-membrane complex

Dear All,

I just started looking at shock propagation in protein-membrane system using Lammps, and found that there are several ways (commands) available in lammps to do so:

(1) In Oscar’s tutorial " A beginner’s guide to the modeling of shock/uniaxial/quasi-isentropic compression using the LAMMPS molecular dynamics simulator,"
they create a piston using a few layers of atom and give it a constant speed to generate a shock and using command:

fix 1 all nve

velocity piston set 0 0 v_Up sum no units box

fix 2 piston setforce 0.0 0.0 0.0

My question is: is “fix move” also able to generate shock in this manner (i.e. move the piston region with some speed)?

(2) “fix wall/piston” command and "fix wall/reflect command " can also generate shock waves.

My questions is: will the characteristics of the shock wave generated by (1) and (2) the same? which method is preferred for bio-molecules system?

Thank you very much,

Lili

yes, you can move atoms with fix move.

Steve

My questions is: will the characteristics of the shock wave generated by (1) and (2) the same? which method is preferred for bio-molecules system?

comment : I would rather use Fix/Piston rather than fix fix/Wall…to generate a shockwave … Method (1) and (2) should produce the same type shockwave, The initial conditions are what mostly affect the characteristic of the shockwave e.g You could either give the piston a RAMP speed or you could maintain a constant speed,etc… The FIX/PISTON command is like having a infinite mass layers of atoms …

which method is preferred for bio-molecules system?

NO idea …

Thanks Steve and Oscar!

Oscar, may I ask a following question regarding your comment on “fix wall/piston command?” In the shock wave script you provided in your tutorial, is there any “piston size effect on the shock?” i.e. size of the region you make as piston. And the “fix wall/piston command” will avoid such effect since it is an infinite-mass piston?

Many thanks for sharing your experience.

Lili

I’ll try to give you my $0.02 worth.

Fix wall/piston and fix wall/reflect do very similar things by having a wall with infinite impedance and your material collide together. Fix wall/piston has the wall impact the material, while with fix wall/reflect the material impacts the wall. Shockwaves are generated in the same way with both fixes. Wall/piston is limited to shock in z-direction, while with wall/reflect you can have the shockwave in any direction.

If you create a piston that is made with real atoms, the impedance is still infinite and hence similar to wall/piston and wall/reflect if the followings are satisfied, 1) the piston atoms are made rigid, 2) the piston keeps moving forward even after the impact (supported shockwave).

Ray

Thanks Ray for the neat explanation. It makes more sense now. -Lili