SMD negative forces

From: Seibold, Steve Allan (stevesei_at_ku.edu)
Date: Fri Mar 29 2019 - 08:37:03 CDT

I have a question on Steered MD. I have been doing multiple pulling simulations and noticed that every time I restart the pulling simulation, I get hundreds of beginning steps with a negative force and hence, in the VMD representation, the system "falls" back from its initial position (i.e. relaxes to its start position) before it starts pulling (with positive force) again. Why is this? Is it because the output (used for restarting) contains no force history? Is there a way to stop this? Am I doing something incorrect?

Thanks Steve

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