AMBER Archive (2008)

Subject: Re: AMBER: Jarzinsky relationship

From: E.M. (pckboy_at_gmail.com)
Date: Thu May 08 2008 - 05:58:10 CDT

Sweet!

Thanks for the timely advice, I was becoming sad at those
PMF shapes. Exponential averaging saved the day

E
Adrian Roitberg wrote:
> The computed work is OF COURSE dependent on the velocity ! It must be,
> or the whole apparatus of thermodynamics break down.
>
> At infinitely slow pulling velocity, the work is exactly equal to the
> free energy for the process.
> For ANY finite velocity there is dissipative work, and its value
> increases in a non-trivial way with the pulling speed.
>
> The application of the Jarzinsky relationship is supposed to fix that.
> There are tons of references, but you can try reading:
>
> "Free Energy calculations with non-equilibrium methods. Applications
> of the Jarzynski Relationship”. Hui Xiong, Alejandro Cresp, Marcelo
> Marti, Dario Estrin and Adrian E. Roitberg. Theoretical Chemistry
> Accounts. 106(1-3): 338-346 (2006)
>
> You will need to run MANY independent simulations pre-equilibrated
> with a restraint at the original distance. Then you do an exponential
> average of the work (at the proper temperature).
>
> Please make sure you applied bugfix.32 to the amber 9 code if you are
> pulling more than 100 angstroms.
>
> a.
>
> PS: for ULTRA experts, there is a correction one can do to the whole
> Jarsynki relationship, defined by Szabo and Hummer in PNAS around 200)
> or 2001. Do not touch if you are not really familiar with the process
> already !
>
>
>
> E.M. wrote:
>> Hello A
>>
>> I am scared....that means that the computed work is dependent on the
>> velocity applied
>> which sounds strange to me....there should be a way to factor out the
>> work done by
>> the biasing force.
>> I ran various tests and it turns out that the higher the rate of
>> motion of the force,
>> the higher the work I get, . . . Is that correct?.
>>
>> The free energies I am computing should be flat at the end, but
>> instead it looks as
>> if the biasing work has to be subtracted.
>>
>>
>> puzzled E.
>>
>> Adrian Roitberg wrote:
>>>
>>>
>>> E.M. wrote:
>>>> Hello,
>>>>
>>>> I am doing some pulling experiments using Jarzinsky's relationship,
>>>> the output file using AMBER9 is something like
>>>>
>>>> x xo whatever work
>>>>
>>>> My question is, do I have to substract the biasing potential after
>>>> I get the output
>>>> or that is taking care of by the program?. I just want to make
>>>> sure I understand
>>>> what is going on here.
>>>>
>>>>
>>>> Regards
>>>>
>>>> E.M.
>>>
>>> Hi,
>>>
>>> The 'wathever' in the list is the crucial factor, in fact it is the
>>> only one one computes !
>>>
>>> It is the external force applied by the external spring (as defined
>>> in the input file). Basically, it is k*(x-x0)
>>>
>>> Work is the integral of that force over the run, so there is no need
>>> to subtract the biasing potential. The subtraction would be needed
>>> only if work was computed from the spring energy, which is not.
>>>
>>> a.
>>>
>>
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