From: Raul Alcantara (realcant_at_artsci.wustl.edu)
Date: Wed Apr 19 2006 - 17:07:05 CDT
Lewyn, Peter and Jerome:
I appreciate your quick response and your helpful comments... I will
take a look at the tcl scripts, it sounds pretty cool...
And about convergence of the work yes I was a bit worried about that
myself I was hoping to carry the pullings as slow as possible as not to
drive the system too far out of equilibrium. I was thinking of checking
convergence by running trajectories in both directions one with the
ligand going in and one with the ligand going out, that would tell me
that I have converged the free energy for the path.
Thanks again...
--Raul
On Wed, 2006-04-19 at 23:20 +0200, Jérôme Hénin wrote:
> Raul,
>
> In the spirit of what Peter suggests (using a Tclforces script), you could use
> the ABF sampling method with a custom reaction coordinate. This should remove
> the issue of reconstructing the PMF from nonequilibrium work data. Coding a
> new reaction coordinate for the code distributed with NAMD is a simple matter
> of adding a Tcl file defining a few procedures. When writing such a file,
> existing reaction coordinate should provide useful templates.
>
> Please let me know if you need help doing this.
> Jerome
>
> Le Mercredi 19 Avril 2006 21:00, Peter Freddolino a écrit :
> > You may, however, be able to avoid playing with the source code by using
> > tclforces (http://www.ks.uiuc.edu/Research/namd/2.6b1/ug/node32.html)
> > instead; you can get it to work along an arbitrary path if you're
> > careful. However, Lewyn's comments on calculating energies still apply.
> > Peter
> >
> > LEWYN LI wrote:
> > > Raul,
> > >
> > > I have always shied away from playing with the source code,
> > > because I never knew if I have inadvertantly introduced errors into
> > > the program.
> > >
> > > On a more theoretical level: since work is not a state function,
> > > its value depends on the speed at and the path along which you pull
> > > the ligand out of the protein. Therefore, it would be tricky to
> > > compare the work value from simulations to experimental data. You
> > > could try to apply the "Jarzynski Equality" and calculate the free
> > > energy, but this might require many, many trajectories (depending on
> > > how far the system is out of equilibrium and other considerations) and
> > > its convergence is difficult to verify.
> > >
> > > Hope this helps!
> > >
> > >
> > > LEWYN
> > >
> > > On Wed, 19 Apr 2006, Raul Alcantara wrote:
> > >> Hello:
> > >>
> > >> I have the following problem: I want to find the average work done to
> > >> pull a small ligand through the matrix of a protein... however the
> > >> possible escape path is not a straight line. So my question to any
> > >> people who have played with the source code is it worth my effort to
> > >> modify the code to do a pulling experiment in a curved path (would this
> > >> severely hurt performance) or would I just be better off by breaking the
> > >> curve into smaller linear segments and doing independent pulling
> > >> experiments for each of those.
> > >>
> > >> Thank you
> > >>
> > >> --
> > >> Raul E Alcantara
> > >> Washington University in St Louis
> > >> Center for Computational Biology
> > >> 700 S Euclid Ave
> > >> Saint Louis MO 63110
> > >>
> > >> Tel (314) 362-8778
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