FEP Rattle Error

From: Ebru Çetin (ebrucetin.ku_at_gmail.com)
Date: Sun Nov 11 2018 - 17:07:51 CST


I am trying to rerun some windows on FEP calculations. I have done the
simulations from the beginning without a problem, and now I am trying to
repeat some problematic windows.

In some cases, they give an error due to RATTLE Algorithm. I have tried
increasing the box size, increasing margin, disabling wrapAll, and changing
rigidbonds to water and time step to 1 fs. When I do change rigidbonds and
timestep together error changes to atoms moving too fast.

Also, I minimized the system that I get after the equilibration of the
first run. I have gone up till 1000 steps since I had minimized it at the
very beginning 40000. But it didn't solve the problem as well.

I will really be grateful for your help to workaround this problem.



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