From: Luthur Cheung (luthur_at_jhu.edu)
Date: Wed Jun 06 2012 - 08:31:43 CDT
Hi, I was using the SMD to unbind two proteins under a constant pulling
velocity. I extracted the pulling force by following the "ft.tcl" script
mentioned in the tutorial. At the beginning, the pulling force was fine
and increased as one of the protein under pulling by the SMD atom. Later
on, when these two proteins were separated, the pulling force started to
slowly decrease. However, the value didn't drop to zero even though the
two protein molecules were already far apart with each other.
Let me put some numbers here in case that help for analyzing my problem:
The pulling force will slowly decrease to ~1000 pN and stayed there
Spring constant k is 1 to 4 kcal/mol/A^2
Pulling velocity is 0.0001 to 0.00005 A/step
Standard time step = 2 femtoseconds
Does anyone know what causes the pulling force not decreasing to zero
while the two proteins are already unbound? If it is necessary, I could
also upload the force-time curve. Thanks!
Best Regards,
Luthur
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