[lammps-users] Force vs displacement of polypeptide

Hi,

I would like to investigate the strength of various polypeptide secondary structures (beta-sheets, alpha-helix) by fixing one end of the polymer to a constant position and applying a constant velocity to the other end so the force vs displacement can be monitored.

I’m wondering if anyone has any advice in how to perform this simulation.

My initial guess is to use the fix move command with linear style in the direction I want to pull but I’m not sure how I would constrain the other end of my polymer from moving.

If you know of any tutorials or have any general help, it would be greatly appreciated.

Thanks,
Joe

Hi,

I would like to investigate the strength of various polypeptide secondary
structures (beta-sheets, alpha-helix) by fixing one end of the polymer to a
constant position and applying a constant velocity to the other end so the
force vs displacement can be monitored.

I'm wondering if anyone has any advice in how to perform this simulation.

this sounds like a job for "fix smd"

My initial guess is to use the fix move command with linear style in the
direction I want to pull but I'm not sure how I would constrain the other
end of my polymer from moving.

you can exclude those atoms from time integration or zero out
forces and velocities. "fix smd" would also allow a "couple" mode,
where you can pull at both ends simultaneously and thus giving
your double the statistics and no fixing of atoms required.

If you know of any tutorials or have any general help, it would be greatly
appreciated.

the papers referred to on the fix smd documentation have very detailed
descriptions of the steered MD process and discuss sources of errors
and accuracy as well.

cheers,
    axel.