Re: Qwikmd ABF Question

From: João Ribeiro (
Date: Wed Jul 04 2018 - 08:08:10 CDT

Do you create the bilayer with QwikMD? When creating the bilayer, the
"Minimal Box" option should be blocked. Is this not the case?

On Wed, Jul 4, 2018 at 2:46 AM McGuire, Kelly <> wrote:

> 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*

João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
+1 (217) 3005851

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