RE: [EXTERNAL] Re: constant pulling velocity in SMD

From: Jiao, Dian NMN (-EXP) (
Date: Thu Apr 26 2012 - 23:10:55 CDT

This is exactly the tutorial I was following. The parameters were set the same with SMDvel 0.00001 and SMDk 5. I doublechecked, I used 0.00001 for the velocity which is 10A/ns. Even if it is 100 A/ns, isn't it odd for the ion to travel ~10 A in 50 fs (approximately 20 micro meter/ns)? I think the force constant I use here is pretty small and hence shouldn't have a dramatic affect on the speed of the ion either.

From: JC Gumbart []
Sent: Thursday, April 26, 2012 5:15 PM
To: Jiao, Dian NMN (-EXP)
Subject: [EXTERNAL] Re: namd-l: constant pulling velocity in SMD

The velocity is in A/timestep. Assuming you're using a 1 fs timestep, that means you're pulling at the rate of 100 A/ns, 10x what you expect.

How well SMD controls the speed depends on the size of the force constant. See the tutorial Forcing Substrates Through Channels here:

On Apr 26, 2012, at 11:33 AM, Jiao, Dian NMN (-EXP) wrote:

Hi, I was trying to pull this metal ion through an ion channel along Z-axis in SMD simulation. SMDvel was set at 0.0001, which means it will travel around 10 A in 1ns. However, my ion travels a whole lot faster. It is first placed near the top of the channel (extracellular surface), it goes from 15.233 to 7.753 (z direction) in merely 50 fs. It doesn't slow down until it hits this spot where the binding between the ion and the lumen facing residues (5 Glu) is very strong. This position is fairly close to the bottom of the channel (intracellular surface). The ion seems to be stablized there and never gets past this position throughout 5ps simulation. Isn't SMDvel supposed to control the speed of the ion moving? Why is it still going so fast? What do I do to make it easy for the ion to escape the binding of that glutamic ring and keeps going down? Thanks in advance.

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