Re: Qwikmd ABF Question

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Wed Jul 04 2018 - 19:25:30 CDT

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> 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>
> *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> 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
> +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
+1 (217) 3005851

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