From: Raul Araya (arayasecchi_at_gmail.com)
Date: Wed Apr 06 2011 - 13:13:58 CDT

Dear VMD users:

Im interested in rendering electrostatic potential maps such as those
described in : "Imaging alpha-hemolysin with molecular dynamics: Ionic
conductance, osmotic permeability and the electrostatic potential map".
Aleksij Aksimentiev and Klaus Schulten. Biophysical Journal, 88:3745-3761,
2005, and other papers. My questions regarding the generation of such maps
are:

1) They make use of the PMEpot plugin, but is there a way to use it with
bigdcd i order to get an average of al frames in a MD?

2) In the mentioned paper the authors comment that the average is done over
the MD and also over the "sevenfold symmetry of a-hemolysin", how does this
averaging is made? In my case I'm working with an hexameric trans-membrane
channel protein.

3) and this is a very technical question: How do you get from one 3d .dx
potential map to the 2d contour maps depicted in the mentioned paper (an in
others) ??

Thanks.

Raúl Araya Secchi
B.Sc Molecular Biotechnology.
Molecular Biotechnology Engineer.
PhD Student (Biotechnology Program. UNAB, Chile)
Computational Biology Lab (DLab)
Center for Mathematical Modeling (CMM)
Facultad de Ciencias Físicas y Matemáticas.
Universidad de Chile.