# Re: Jarzinsky's equation

From: Fatemeh Khalili (akhalili_at_ks.uiuc.edu)
Date: Tue Dec 07 2010 - 12:39:45 CST

If that's the only force you are applying to the system, then that is your
external work.

-Fatemeh

On Fri, Dec 3, 2010 at 2:08 PM, Gianluca Interlandi <
gianluca_at_u.washington.edu> wrote:

> 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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