Re: Constant Velocity Pulls

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Fri Feb 22 2019 - 12:58:37 CST

Ok, so if I'm comparing 3 different ligands in the same protein, the spring will stretch for all three until they are pulled at say 1 A/ns if that is the velocity I chose. What happens to the spring/velocity as the ligand collides/interacts with sidechains along the path until it is out of the protein? Does the spring length adjust to keep the ligand at 1 A/ns? Thanks for the response!

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
Sent: Friday, February 22, 2019 11:51:41 AM
To: McGuire, Kelly; namd-l_at_ks.uiuc.edu
Subject: RE: Constant Velocity Pulls

Hi Kelly,

Wouldn't constant velocity pulling imply that they all leave when they are told to by the ridiculously high force applied? Like, if you pull at 1A/ns, they will all be 3A away in 3ns... Am I missing something? The *forces* might be comparable, but the leaving times certainly are going to be meaningless.

-Josh

On 2019-02-22 09:04:53-07:00 owner-namd-l_at_ks.uiuc.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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