Re: Constant Velocity Pulls

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Fri Feb 22 2019 - 13:12:56 CST

Thanks BKR, I had not hear of RAMD. This looks promising.

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Brian Radak <brian.radak_at_gmail.com>
Sent: Friday, February 22, 2019 12:06:09 PM
To: namd-l; McGuire, Kelly
Subject: Re: namd-l: Constant Velocity Pulls

Hi Kelly,

Unfortunately, I think this is a question much better answered by the literature than by anyone particular on the listserv.

One thing you might consider is the new RAMD<http://www.ks.uiuc.edu/Research/namd/2.13/features.html> feature in NAMD 2.13 (look at the bottom of the feature summaries).

HTH,
BKR

On Fri, Feb 22, 2019 at 11:00 AM McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:

  I keep being told that I should resist using constant velocity SMD when looking for ligand/protein separation leaving times, but with no explanation. Why can't I use constant velocity pulling to compare leaving times for different ligands in a protein?

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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