Re: Ion Channel Jarzynski

From: JC Gumbart (
Date: Thu Aug 10 2006 - 20:28:55 CDT

Your first problem could be addressed using tclforces (along with a
separate script) to pull your molecule at a constant velocity and
then use SMD with a velocity of zero in the z direction to restrain
your protein's center of mass.

Does that make sense?

On Aug 10, 2006, at 5:56 PM, Alessandro Cembran wrote:

> Hi,
> I am trying to compute the PMF for the passage of a molecule
> through a protein channel by using the Jarzynski equality (the
> constant velocity pulling through a dummy atom scheme). I've read
> several papers on this topic, but I couldn't find the fine details
> on how to set up the constraints. I also ran the deca-alanine,
> ubiquitine and nanotubes tutorials to get acquainted with the
> methods but I still have some things that need to be clarified:
> - I need to pull down the channel the molecule through the dummy
> atom that moves at a constant velocity, and I can do that with a
> tcl script. But this is not enough, I need a second handle to keep
> the protein from moving (I realized that in 4ns of simulation the
> protein and the membrane can move several angstroms along the z
> direction, as somebody else noticed previously on this forum). In
> the deca-alanine and ubiquitine systems this second handle was
> easily provided by fixing an atom, but in this case it is not
> possible. It is the center of mass of the protein that should be
> fixed, at least along the z direction and I don't think that is
> possible. Would it be meaningful to add a restraining force to the
> COM of the protein through a tcl script? If yes, how would this
> additional fluctuating force affect the computed PMF?
> - In this article (Amaro,Tajkhorshid,Luthey-Schulten - Proc. Natl.
> Acad. Sci. USA 2003, 100(13), 7599.) I read that there is no
> substantial difference in computing a PMF by Jarzynski equality
> with a NPT or NVT simulations. I was wondering if anybody else has
> any comments about that.
> Thanks in advance,
> Alessandro
> --
> Alessandro Cembran,PhD
> Post Doctoral Associate
> Univ. of Minnesota, Dept. of Chemistry
> G2, 139 Smith Hall 207 Pleasant St SE
> Minneapolis, MN 55455-0431
> Office: +1 612-625-4319

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