Re: Jarzinsky's equation

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Fri Dec 03 2010 - 14:08:00 CST

Hi Fatemeh,

You are saying that this works even if the simulation was done at constant
force? Isn't work simply going to be proportional to my reaction
coordinate, which in my case is exactly the distance between the atoms
that I'm pulling apart?

Gianluca

On Fri, 3 Dec 2010, Fatemeh Khalili wrote:

> By having the force and the extension that the force is applied to you can always calculate
> the external work. You just need to write the work as a function of your reaction
> coordinate for your integration, when using Jarzynski. 
> -Fatemeh
>
> On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u.washington.edu> wrote:
> Hi Fatemeh,
>
> Thanks for replying. The simulations were not performed at constant velocity
> but at constant force. Is it still possible to apply Jarzinsky's equation?
> Also, according to your publication I have to integrate the work done along the
> trajectory. How do I do that?
>
> Thanks!
>
>     Gianluca
>
>
> On Thu, 2 Dec 2010, Fatemeh Khalili wrote:
>
> Hi Gianluca,
> To use Jarzynski's equality you need to calculate the work done by the
> external forces you
> apply to the system.  The SMD forces (your external force) are written in
> your log file.
> Proper distances (spring extension/contraction) can also be extracted
> from the log file and
> your trajectory. By knowing the expansion of the spring, you can
> calculate the work applied
> to your system.
>
> -Fatemeh
>
>
>
>
> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi
> <gianluca_at_u.washington.edu> wrote:
>      I would like to calculate the free energy of a protein-protein
> complex using
>      the Jarzinsky's equation from already performed SMD simulations. I
> would be
>      happy if somebody could point me out to some scripts which help me
> perform
>      that.
>
>      In a previous thread in response to somebody asking the same
> question
>      (http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/2719.html)
>      it was mentioned that NAMDenergy can calculate all sorts of
> energies. However,
>      I cannot find any option for NAMDenergy which does that.
>
>      Thanks!
>
>          Gianluca
>
>      -----------------------------------------------------
>      Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>                         +1 (206) 685 4435
>                         http://artemide.bioeng.washington.edu/
>
>      Postdoc at the Department of Bioengineering
>      at the University of Washington, Seattle WA U.S.A.
>      -----------------------------------------------------
>
>
>
>
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>                    +1 (206) 685 4435
>                    http://artemide.bioeng.washington.edu/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------
>
>
>
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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