Re: Qwikmd ABF Question

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Wed Jul 04 2018 - 11:21:21 CDT

The reason I still use CHARMM GUI is because QwikMD doesn't have DMPC lipid as a choice yet, and we needed that for this ABF.

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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From: João Ribeiro <jribeiro_at_ks.uiuc.edu>
Sent: Wednesday, July 4, 2018 7:08:10 AM
To: namd-l_at_ks.uiuc.edu; McGuire, Kelly
Subject: Re: namd-l: Qwikmd ABF Question

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 <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> 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

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João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
http://www.ks.uiuc.edu/~jribeiro/
jribeiro_at_ks.uiuc.edu<mailto:jribeiro_at_ks.uiuc.edu>
+1 (217) 3005851

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