Re: constant pulling velocity in SMD

From: Axel Kohlmeyer (
Date: Wed Apr 25 2012 - 17:16:15 CDT

On Wed, Apr 25, 2012 at 3:41 PM, 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

nope. the manual says, SMDvel is given in angstrom per timestep.
assuming a 1fs timestep, you'll get 0.1A per picosecond,
correspondingly more for a shorter timestep.

> 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

5ps is *nothing*. in any case, before jumping to conclusions,
you should first equilibrate your system with the metal ion held
in place (and the channel plus membrane).

> 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.

one reason seems to be your miscalculation of the
velocity, but you didn't say what force constant you
are using for the restraint of the pulling group to the
SMD reference. if that force constant, isn't chosen
reasonably, all kinds of strange things can happen.


> Dian

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:21:55 CST