Re: Jarzinsky's equation

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Dec 02 2010 - 14:35:54 CST

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.
-----------------------------------------------------

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