Re: Qwikmd ABF Question

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Thu Jul 05 2018 - 10:48:41 CDT

Hey Joao, thinks for the link. I just wen through the tutorial for the membrane section, and it does mention being able to use other lipids besides POPC and POPE. However, it doesn't describe a method for changing the POPC to say DMPC. Would the simplest way be to open the POPC membrane pdb file generated with the membrane builder plugin in QwikMD, and then use Structure Manipulate to change the lipid type? Or is there another way to change the POPC to DMPC? Thanks!


Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602


________________________________
From: João Ribeiro <jribeiro_at_ks.uiuc.edu>
Sent: Thursday, July 5, 2018 7:03:31 AM
To: McGuire, Kelly
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: Qwikmd ABF Question

Hi Kelly,

there is a membrane-protein tutorial that you can follow at http://www.ks.uiuc.edu/Training/Tutorials/#memprot. NAMD does not detect the axis of the membrane in any simulation. The important step here is to define the periodic boundary conditions to ensure that the membrane is "infinite", so right at the pbc limits, and you don't get water in the hydrophobic region
​ of the membrane​
. All these steps are taken care during the structure preparation in VMD
​ ​(see tutorial)

and in the definition of the pbc in the configuration files of NAMD. Additional options might be useful such as useConstantRatio

.

I hope this helps

Best

João


On Wed, Jul 4, 2018 at 7:35 PM McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:

Thanks for the reply. In your experience, what is the best way to generate a bilayer with lipids that aren't available in QwikMD yet, but that NAMD can detect the axis of the membrane, so that I can avoid the problems that come from mixing programs like CHARMM GUI with VMD/NAMD? Thanks!


Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602


________________________________
From: João Ribeiro <jribeiro_at_ks.uiuc.edu<mailto:jribeiro_at_ks.uiuc.edu>>
Sent: Wednesday, July 4, 2018 6:25:30 PM
To: McGuire, Kelly
Cc: namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>
Subject: Re: namd-l: Qwikmd ABF Question

Regarding QwikMD and Charmm-Gui, I already comment on that on one of your previous questions: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2017-2018/2032.html

From QwikMD user Guide

  * Minimal Box: Rotate the system and apply a simple solvent box padding distance, instead of the formula described in the "MD/MDFF Protocol box" description. The usage of this option should be used carefully and the "Buffer" distance should be increased to account system rotation/tumble during the simulation (see VMD solvate plugin<http://www.ks.uiuc.edu/Research/vmd/plugins/solvate/>).

QwikMD is doing what you are asking it to do :)

Best

João

On Wed, Jul 4, 2018 at 6:44 PM McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:

I don't suppose there is a way to turn off the rotation after selecting the Minimization Box option in QwikMD?


I get this in the VMD log after I click prepare in QwikMD:


"The system was rotated by 360.0 degrees around Z axis and 350.0 degrees around X axis."


I don't want it rotated around the x or y axes...


Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602


________________________________
From: João Ribeiro <jribeiro_at_ks.uiuc.edu<mailto:jribeiro_at_ks.uiuc.edu>>
Sent: Wednesday, July 4, 2018 7:08:10 AM
To: namd-l_at_ks.uiuc.edu<mailto: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



--
……………………………………………………...
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


--
……………………………………………………...
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


--
……………………………………………………...
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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