Constant Velocity SMD Question

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Thu Feb 21 2019 - 01:32:02 CST

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  In your opinion/experience, would it be more accurate to use the equilibration.restart or free molecular dynamics restart files for a steered molecular dynamics simulation? I ask because my ligand that I want to pull out of a channel takes on a different confirmation in a free MD simulation (no restraints) than in the equilibration simulation (due to restraints applied). I wonder if including this different confirmation as a starting point for the SMD would change the result of the constant velocity SMD, and if that would be more realistic than starting from a restrained equilibration confirmation...

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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