SMD for predetermined Umbrella sampling Windows

Date: Mon Nov 08 2021 - 22:17:55 CST

I have inherited an old system with preconfigured windows for that system, where the previous owner is unsure how they generated these windows. I already have the windows I would like configured based on a previous simulation but now have an updated starting structure. How would I go about making this starting structure to work with my current window configurations? I saw that:

The most common approach is to use an initial SMD pull to cover your reaction coordinate space (center = initial value, targetCenter = final value), and then pick frames from that pull to seed your umbrellas.

But I cannot do this option, it would be far too difficult to implement as there is a certain order of binding that needs to occur, and I am going to be sampling roughly 400 different configurations.
Essentially can I take my starting structure, apply a quick pulling simulation to get my chlorides in the right position? How would I go about this? The tutorial files only have you pulling one thing all the way through via SMD and that will not work for my system. I just want a way to pull the starting equlibrated structure into the window, and then be able to run production on it after running a quick pulling simulation to get my chlorides in the right spot.


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