Re: custom pulling path

From: Peter Freddolino (
Date: Wed Apr 19 2006 - 14:00:56 CDT

You may, however, be able to avoid playing with the source code by using
tclforces (
instead; you can get it to work along an arbitrary path if you're
careful. However, Lewyn's comments on calculating energies still apply.

LEWYN LI wrote:

> Raul,
> I have always shied away from playing with the source code,
> because I never knew if I have inadvertantly introduced errors into
> the program.
> On a more theoretical level: since work is not a state function,
> its value depends on the speed at and the path along which you pull
> the ligand out of the protein. Therefore, it would be tricky to
> compare the work value from simulations to experimental data. You
> could try to apply the "Jarzynski Equality" and calculate the free
> energy, but this might require many, many trajectories (depending on
> how far the system is out of equilibrium and other considerations) and
> its convergence is difficult to verify.
> Hope this helps!
> On Wed, 19 Apr 2006, Raul Alcantara wrote:
>> Hello:
>> I have the following problem: I want to find the average work done to
>> pull a small ligand through the matrix of a protein... however the
>> possible escape path is not a straight line. So my question to any
>> people who have played with the source code is it worth my effort to
>> modify the code to do a pulling experiment in a curved path (would this
>> severely hurt performance) or would I just be better off by breaking the
>> curve into smaller linear segments and doing independent pulling
>> experiments for each of those.
>> Thank you
>> --
>> Raul E Alcantara
>> Washington University in St Louis
>> Center for Computational Biology
>> 700 S Euclid Ave
>> Saint Louis MO 63110
>> Tel (314) 362-8778

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