Dear All,
Firstly I would like to give a context for my simulation. I am trying mechanically unfold a polymer of 100 beads using fix smd and colvars(for testing purpose). I have fixed one end of polymer by excluding the bead from time integration. Now I want a force extension curve for the polymer. fix smd has 7 output where I can get a component of force as well as the magnitude of force. I am doing a constant velocity simulation with a velocity of -0.0001 and the spring tethered at (100, 0, 0). Now when I plot the force acted on the atom attached to the spring. I get the following plot.
When I change the x-axis scale i see a pattern in force over time.
Also the polymer unfolds overtime correctly.
My questions are as follows:
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Is this behaviour of force normal as in, is this supposed to be in this way, in a pattern? I understand that the force applied is by a spring. But I did not expect force like this. I have performed simulations by adding a external force at one end of polymer and equilibrating it. (The force is added every timestep). I expected the general trend of force to increase over time.
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I also used colvars to do the same. I know its better to use colvars than fix smd. One thing I noticed is that the end to end behaviour in fix smd and colvar was different. How different is colvars when using moving harmonic restraint than fix smd procedure wise?
Thank you for your time! I hope that I have not left anything unclear in my post. I am attaching the input files for the same.
LAMMPS version: 2Aug2023
colvars.inp (413 Bytes)
cv_r1.inp (1.5 KB)
smd_r1.inp (1.8 KB)