VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Wed Jun 20 2018 - 18:07:50 CDT

Great, thank you for that link!

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, June 20, 2018 4:56:49 PM
To: McGuire, Kelly
Cc: Vmd l
Subject: Re: vmd-l: QwikMD Restraints Question

Hi Kelly,

QwikMD has an extense User's Guide at http://www.ks.uiuc.edu/Research/vmd/plugins/qwikmd/ and there is a direct link this page on QwikMD's webpage as well (http://www.ks.uiuc.edu/Research/qwikmd/). You can find almost all information related to the commands and functions of QwikMD there.

Your question is answered at http://www.ks.uiuc.edu/Research/vmd/plugins/qwikmd/#advprot. Those restraints are to harmonic restraints to the coordinates of the atoms defined by the atom selections.

I hope this helps

Best

João

On Wed, Jun 20, 2018 at 5:38 PM McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:

QwikMD offers the ability to select pre-defined restraints. Some of them are obvious, but is there a description

somewhere of what those pre-defined restraints selections are? For example, the pre-defined protein selection, is

that the center-of-mass of the protein? I am needing to apply a restraint to the center of mass of my protein, and I know

this can be done with coding/colvars, but hoping QwikMD has that as a pre-defined selection. Thanks!

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