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

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Apr 20 2009 - 08:41:22 CDT

On Mon, 2009-04-20 at 11:16 +0300, Mert Gür wrote:
> 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

mert,

not in my understanding. if you do umbrella sampling you should
not constrain any other direction but the reaction coordinate.
if your system deviates from it randomly, it should average out,
you just have to run long enough to make sure you are converged;
if it deviates systematically, you have chosen the wrong reaction
path. from all you are telling us, i am tempted to believe that
the latter is the case.

cheers,
   axel.

> 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 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>
>
> > > 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"
> > >
>
>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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