Re: custom pulling path

From: LEWYN LI (
Date: Wed Apr 19 2006 - 13:52:00 CDT


         I have always shied away from playing with the source code,
because I never knew if I have inadvertantly introduced errors into the

         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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