From: Ishaan Roy (royi_at_uchicago.edu)
Date: Wed Jun 30 2021 - 20:44:23 CDT
Hi,
I am running an ABF simulation on a membrane protein to find the binding free energy. In one of the systems, when running ABF on the tilt angle colvar, the protein flips over almost 180 degrees within the membrane. However, in other systems, the protein stays within a smell tilt angle range in the membrane when running the ABF on it. The tilt colvar currently has an upper and lower limit of 1 and -1. Could this problem be a result of the ABF countering interactions that would normally keep the protein in a natural orientation? If so, then to what values should the upper and lower limit be changed?
Thanks,
Ishaan
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