VMD-L Mailing List

From: Rafael Bernardi (rcbernardi_at_auburn.edu)
Date: Tue Jan 05 2021 - 22:23:27 CST

Hello Tiglath,

If you are using the “Easy Run” tab of QuikMD, the so-called Equilibration will include minimizations steps. The info button right next to the Equilibration check box that you have selected clearly states that “QwikMD automatically runs 1000 steps of Energy Minimization, a temperature ramp in which the temperature of the system is raised from 60K to the target temperature … an additional 1.0 ns of equilibration simulation.”

If you want to have more control over the options, please used the “Advanced Run” tab.

Best wishes,

Rafael

……………………………………………………………………...
Rafael C. Bernardi
Biophysics Cluster - Department of Physics at Auburn University
NIH Center for Macromolecular Modeling & Bioinformatics
rcbernardi_at_auburn.edu<mailto:rcbernardi_at_auburn.edu>
rcbernardi_at_ks.uiuc.edu<mailto:rcbernardi_at_ks.uiuc.edu>
www.ks.uiuc.edu/~rcbernardi<http://www.ks.uiuc.edu/~rcbernardi>
+1 (334) 844-4393





From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Tiglath Moradkhan <moradkhantig_at_gmail.com>
Date: Tuesday, January 5, 2021 at 5:10 PM
To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Running equilibration MD simulation

Hi VMD community

I just wanted to clarify that if I select the equilibration protocol in the qwikMD plugin that only the equilibration step will be run. The reason I'm asking is that when I run the simulation, it starts with minimization first. Is this right or do I need to do something else so equilibration runs?

Thanks

Tiglath