ABF simulations

From: Raul Araya (arayasecchi_at_gmail.com)
Date: Mon Jul 28 2008 - 14:45:46 CDT

Dear NAMD users: (Specially those related to ABF simulations)

I have been reading the paper from the Shulten group (Henin, Tajkhorshid,
Shulten, Chipot. Biophysical Journal Vol. 94, February 2008 832-839) and Im
interested in performing this kind of methodology to pass a solute trough a
membrane channel. The paper is clear about the ABF method used, and also is
the ABF turotial for NAMD, but nevertheless I will like to get more details
about how the methodology was implemented for this GlpF + Glicerol ABF
simulation. Im interested mostly in how the initial configuration for each
window was established, what type of coordinate was chosen, and in general a
little more detail about the ABF simulation in this particular case.


-- Raúl Araya Secchi
        B.Sc Molecular Biotechnology.
        Molecular Biotechnology Engineer.
        Centre for Bioinformatics CBUC,
        Faculty of Biological Sciences, P. Universidad Catolica de Chile
        Portugal # 49 – ZIP 6513492 Santiago – Chile Phone: + 56 2 6862269;

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