From: Mert Gür (gurmert_at_gmail.com)
Date: Mon Apr 20 2009 - 03:16:39 CDT
Sorry I didn't explain my problem properly.
As you emphasized I divided my reaction coordinates into bins. At each
specific coordinate (bin), I have to aplly an biasing potential to keep it
there. For that case I am using SMD and set the velocity to zero. So I have
an harmonic potential applied along my reaction coordinate(x axis). But it
does not stay on the SMD vector (1 0 0). As you already mentioned it samples
also into the other directions (y and z directions) which as far as my
understanding goes (by reading the literature) we don't want. That is why I
applied a negligble small constraining potential into the x and y
directions.
Using the positional fluctuation values along the reaction coordinates at
each US simulation I construct the PMF via WHAM.
Best,
Mert
On Mon, Apr 20, 2009 at 2:27 AM, Chris Harrison <char_at_ks.uiuc.edu> wrote:
> Mert,
>
> I'm not sure what you mean by "SMD with zero velocity for Umbrella
> sampling.." In typical umbrella sampling the rxn coordinate is divided into
> bins (10 bins is usually a reasonable first guess if you have no a priori
> knowledge of how many bins are needed) and each bin is sampled
> independently; no SMD or pulling velocity needed. You then "merge" the bins
> to construct to PMF via a weighted histogram analysis. Not sure if this
> helped ....
>
>
> 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 19:10:11 +0300
> > From: Mert Gür <gurmert_at_gmail.com>
> > To: Chris Harrison <char_at_ks.uiuc.edu>
> > Cc: NAMD list <namd-l_at_ks.uiuc.edu>
> > Subject: Re: 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: <72cbc58f0904190910g68238254kcae57f28652acb1_at_mail.gmail.com>
> > X-Spam-Status: No, score=-1.1 required=5.0 tests=AWL,BAYES_00,
> > DNS_FROM_RFC_POST,HTML_30_40,HTML_MESSAGE,SPF_PASS autolearn=no
> > version=3.1.7-0+tcb1
> >
> > 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> <
> 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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