From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Sun Apr 19 2009 - 18:27:24 CDT
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" > >
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