Fix deform for Protein tensile tests: Molecules recoiling back after a few steps.

Hello everyone,

I am trying to perform tensile tests on a collagen type I microfibril unit with 3 molecules placed near to each other. I am using the command fix deform and the syntax I am using is :

fix 2 all deform 1 z vel 0.005 remap v units box
fix 3 all nvt/sllod temp 300.0 300.0 100.0

After a certain point in time, the molecule is recoiling back and the simulation box is getting deformed as seen during the periodic image in VMD and also in the log file under the tab lz.

I would like to know the basics of working of the fix deform command and the how the coordination between the box and atoms take place that the molecule is recoiling back.

if you’re deforming a molecule, why would it not recoil at some point,
presuming it has harmonic bonds. You can’t stretch a molecule indefintely.
Fix nvt sllod is for shearing liquids continuously. It will cause problems
if the fluid is not deforming (forever) with the box deformation.

Steve