Qwikmd ABF Question

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Wed Jul 04 2018 - 02:42:39 CDT

Something I haven't observed with QwikMD is occurring. I us QwikMD to set up the multiple windows I need for my ABF simulation. I create 16 windows where my ligand goes from bulk water on the N-terminus of my bilayer embedded protein, through the protein, and to the C-terminus bulk water. When I use QwikMD to create the solvated bilayer/protein/ligand system on the N-terminus side in bulk water (about 15 angstroms from the bilayer/protein), my bilayer/protein remains perpendicular to the z-axis, which is what I want. My reaction coordinate is along the z-coordinate. However, when I do this at the C-terminus bulk water side (about 15 angstroms into bulk water), QwikMD flips my bilayer/protein/ligand system to be perpendicular to the y-axis. This, I assume, creates problems with calculating a PMF when all of my other windows are perpendicular to the z-axis...I do select Minimal Box and 12 angstrom buffer for all of my windows. Why would QwikMD flip my system like this on the C-terminus bulk water end but not the other end?

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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