[gmx-users] How to dynamically change the "pull-coord1-init" during SMD simulation

[bonjour899]

Hello everyone,


This email is asking for some suggestions. Actually I'd like to conduct a kind of steered molecular dynamics simulation like this:
Fixing one end of a protein, pulling the other end for a certain distance Δx (can be for example 0.5 nm, 0.2 nm ...), relaxing the whole system for sufficient time and then repeating that.
The method I can think of is still using COM pulling code
pull-coord1-type=umbrella
pull-coord1-geometry=diatance
This is like applying a harmonic spring between the two ends of the protein with harmonic potential U=1/2*k*(r-r0)^2 and I think I should modify the parameter "pull-coord1-init" to extend the equilibrium length of the spring for Δx so that I can achieve pulling the protein for Δx (is "pull-coord1-init" like the r0 in the harmonic potential equation? Maybe my understanding of this parameter is wrong?).
However, since I want to pull the protein for a long distance, I should gradually change the equilibrium length, and I have no idea how to dynamically change the "pull-coord1-init" during SMD simulation. Or do I have to restart the simulation with a new .mdp file with different "pull-coord1-init" for each step?


Best regards,
W