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

From: Mert Gür (gurmert_at_gmail.com)
Date: Sun Apr 19 2009 - 11:10:11 CDT

Dear Chris,
It seems that my x-values increases as I wish. As you suggest pulling
faster with a higher force constant seems to be a solution (Now I have fixed
the Jarzynski case :) ) but I also try to use SMD with zero velocity for
Umbrella Sampling Calculations.
In that case the fast pulling option wont be possible.
I should somehow to be able to sample the same reaction coordinates and
obtain a similar PMF for both methods.
Best,

On Sun, Apr 19, 2009 at 6:25 PM, Chris Harrison <char_at_ks.uiuc.edu> wrote:

> Mert,
>
> 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 spring constant to
> achieve an optimal "signal-to-noise" in your force curve.
>
>
> C.
>
>
>
> --
> 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
>
> char_at_ks.uiuc.edu Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar>
> Fax: 217-244-6078
>
>
> Mert Gür <gurmert_at_gmail.com> writes:
> > Date: Sun, 19 Apr 2009 15:56:00 +0300
> > From: Mert Gür <gurmert_at_gmail.com>
> > To: NAMD list <namd-l_at_ks.uiuc.edu>
> > Subject: namd-l: I can't keep my pulling directions the same with the SMD
> > vector
> > Return-Path: char_at_halifax.ks.uiuc.edu
> > Message-ID: <72cbc58f0904190556i3ed67eecke2b3c356b1b5c2e6_at_mail.gmail.com
> >
> > X-Spam-Status: No, score=-2.0 required=5.0 tests=AWL,BAYES_00,HTML_40_50,
> > HTML_MESSAGE autolearn=unavailable version=3.1.7-0+tcb1
> >
> > 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<
> http://adsabs.harvard.edu/cgi-bin/author_form?author=Park,+S&fullauthor=Park,%20Sanghyun&charset=UTF-8&db_key=PHY
> >;
> > Khalili-Araghi,
> > Fatemeh<
> http://adsabs.harvard.edu/cgi-bin/author_form?author=Khalili-Araghi,+F&fullauthor=Khalili-Araghi,%20Fatemeh&charset=UTF-8&db_key=PHY
> >;
> > Tajkhorshid, Emad<
> http://adsabs.harvard.edu/cgi-bin/author_form?author=Tajkhorshid,+E&fullauthor=Tajkhorshid,%20Emad&charset=UTF-8&db_key=PHY
> >;
> > Schulten, Klaus<
> http://adsabs.harvard.edu/cgi-bin/author_form?author=Schulten,+K&fullauthor=Schulten,%20Klaus&charset=UTF-8&db_key=PHY
> >
> >
> >
> > http://adsabs.harvard.edu/abs/2003JChPh.119.3559P
> >
> > 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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