Re: smd force is too high

From: Aron Broom (
Date: Fri Mar 15 2013 - 12:10:55 CDT

Hi Jackie,

I'm not really very familiar with SMD, but have you tried a smaller pulling
velocity? I can imagine that if the pulling velocity is too fast to allow
the system to be in a constant pseudo-equilibrium, you might appear to have
a steeper energy barrier to pulling the protein because you have slowly
relaxing orthogonal degrees of freedom that aren't being given time to
relax. That is, you're crossing the energy barriers associated with those
slowly relaxing degrees of freedom using a path that isn't the lowest
energy one. Again, I'm not terribly familiar with SMD, but this kind of
problem is fairly general to any biased MD and it will generally present
itself as the energy barrier appearing to be much greater than you expected.

The above being said, is the value you are getting really that extreme? I
suppose -0.6 kcal/mol/Ang is effectively the gradient for the binding
energy? If so, what would you be expecting for the actual binding energy
over the distance you want to pull? It seems like a gradient of this
magnitude would only yield a binding energy of at most a few kcal/mol or am
I confused?


On Fri, Mar 15, 2013 at 12:25 PM, Jacqueline Schmidt <> wrote:

> Dear NAMD users,
> I have a question regarding the smd simulation using NAMD. I am pulling
> off a peptide from a surface (surface is fixed) using smd with force
> constant of 6 kcal/mol/Ang^2 and pulling velocity of 5x10^-6 Ang/fs. My
> problem is the forces that are printed in the output are unreasonably highe!
> e.g. at step 100, the center of mass of peptide has been moved ~0.1 Ang in
> z-direction. The smd force printed in the output is fz~-43 and I assume the
> units are kcal/mol/Ang
> but this is so high! Doing a rough calculation for force Fz=k(vt-z+z0)=
> 6(5*10^-6 -0.1) ~-0.6 kcal/mol/Ang
> can anyone please help me with this?
> I will appreciate it
> jackie

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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