Re: I can't keep my pulling directions the same with the SMD vector

From: Chris Harrison (
Date: Sun Apr 19 2009 - 10:25:14 CDT


You need to look at the average x-coord value. Is it increasing? There's nothing that by default restrains the pulled particle to specific values of y & z when pulling in x. So while the x-coord value may increase, the particle may in fact freely sample the available y & z coordinates. The spring constant and force constant or pulling velocity can notably influence the degree or extent to which sampling can occur in y & z for a given value of x when pulling in x. Assuming a constant velocity SMD, if you pull faster with a strong spring constant the particle will "not have enough time and spring-flexibility" to sample y & z coords that significantly deviate from those of the initial structure ... but this will of course lead to poorer sampling and possibly a noisier force curve. It is a balancing act, the "tipping point" of which must be determined empirically for each system. One approach is to do some very fast pullings to test, then lower your pulling velocity and retest, then possibly refine your s
pring constant to achieve an optimal "signal-to-noise" in your force curve.


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                          Voice: 217-244-1733              Fax:   217-244-6078
Mert Gür <> writes:
> Date: Sun, 19 Apr 2009 15:56:00 +0300
> From: Mert Gür <>
> To: NAMD list <>
> Subject: namd-l: I can't keep my pulling directions the same with the SMD
> 	vector
> Return-Path:
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> I try to evaluate th PMF of unbinding of a protein-protein complex. As was
> suggested for SMD calculations in the following paper, I try to move only
> into the x direction. But I just can't keep my reaction coordinates (which
> is the vector between the fixed atoms and smd atoms)  along the x direction.
> I also tried to aplly an external constraining force of 1/10 in magnitude of
> the SMD spring constant. But after each simulation the vector keeps
> increasing its y magnitude.
> So my question here is how high can I go  with these constraining forces so
> that my reaction coordinate moves strictly along the x direction and still
> makes sense. Or is there any other methodology I missed. I tried to follow
> all the discussion that have been performed previously regarding the SMD
> calculations.
> Best,
> Mert
> Free energy calculation from steered molecular dynamics simulations using
> Jarzynski's equality Park,
> Sanghyun<,+S&fullauthor=Park,%20Sanghyun&charset=UTF-8&db_key=PHY>;
> Khalili-Araghi,
> Fatemeh<,+F&fullauthor=Khalili-Araghi,%20Fatemeh&charset=UTF-8&db_key=PHY>;
> Tajkhorshid, Emad<,+E&fullauthor=Tajkhorshid,%20Emad&charset=UTF-8&db_key=PHY>;
> Schulten, Klaus<,+K&fullauthor=Schulten,%20Klaus&charset=UTF-8&db_key=PHY>
> where it is indicated that:
> "In the simulation, we fix one end of the molecule ~the N atom of the first
> residue! at the origin and constrain the other end ~the capping N atom at
> the C-terminus! to move only along the z axis, thereby removing the
> irrelevant degrees of freedom, i.e., overall translation and rotation"

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