Constant Force Pull

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Thu Dec 13 2018 - 03:44:18 CST

  I am trying to do a constant force pull on my ligand, pulling it out of a protein. I have the backbone atoms and certain atoms in the DMPC membrane constrained. The force on the ligand is 1 kcal/mol/A^2 or 69.479 pN A. As the ligand is moving, the waters on both sides of the membrane expand away from the membrane the simulation stops with the error:

ERROR: Constraint failure in RATTLE algorithm for atom 60956!
ERROR: Constraint failure; simulation has become unstable.

  Before I put a constraint on the membrane, it was separating in opposite directions along the z-coordinate. As for the water, I can't constrain those or the simulation stops with periodic boundary errors. How do I do a constant force pull on a ligand in a protein/membrane/water system?

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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