Fix SMD

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1

Dear Lammps users,

I want to run constant velocity SMD simulations with fix SMD command. Using cvel mode with tether keyword does not seem to work for me as it seems that the distance between tether point and the pulling group increases (or decreases). However, I want the fix group to follow a dummy moving atom (reminiscent of AFM tip) with the help of spring. In AFM the spring length does not change too much, while in cvel with tether keyword the length increases. Thus, it does not work here.

The other option is to use cvel mode with the couple keyword. I have added a dummy atom which has a fixed velocity and would not be thermostatted and it is coupled to the SMD group. Here in the fix SMD command the velocity value is zero. And x, y and z are set to auto. However, I am not sure what is the R0. Should it be the equilibrium length of spring? I read that part of manual several time, but it is a little bit confusing.
This is the part of my lammps script related to SMD:

create_atoms 5 single 29 -0.087 -1.83
group dummy type 5
group rest subtract all dummy
neigh_modify exclude group dummy rest

fix 1 rest nvt temp 310 310 1.0
fix 3 right smd cvel 10 0 couple dummy auto auto auto 10
fix 4 left spring/self 10.0 xyz
fix 6 rest momentum 1000 linear 0 0 0 angular
fix 7 dummy move linear 1e-5 0 0 units box

Yours sincerely
Mahdi

2

This seems mostly due to bad simulation design and parameter choices and not because the features you are using “do not work”.

  1. if you have a dummy atom at constant velocity and want a group of atoms following it, you need fix spring, not fix smd.
  2. if you use fix smd in tether mode with cvel setting, this is identical to scenario 1). in fact, that is how fix smd was tested originally, since fix smd was implemented based on fix spring.
  3. if a group of atoms is not following the reference they are coupled to, check the spring force. your force constant seems rather low and thus it may be expected that the coupled group of atoms is not following immediately. please also keep in mind, the restoring force (and thus the coupling force constant) may need to be very large if the coupled group of atoms is very large and thus heavy. it is intuitive, that you need more force to move a heavier object.
  4. r0 has to be zero in your case (and almost any other use case, it is relic that fix smd inherited from fix spring).

axel.