**From:** Fatemeh Khalili (*akhalili_at_ks.uiuc.edu*)

**Date:** Fri Dec 03 2010 - 13:25:31 CST

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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.
*

*> -----------------------------------------------------
*

*>
*

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