We would like to simulate a protein in an implicit lipid environment,
which for an accurate description is a multi-dielectric environment. Is
there a way to specify many dielectric (e.g. could be on a grid) slabs to
mimic the lipids?
139-74, Beckman Institute
Division of Chemistry and Chemical Engineering
Caltech, Pasadena, CA 91125
There's a fairly detailed discussion of this here:
The basic idea is to generate OpenDX maps which describe the desired
dielectric properties. Often, people will generate initial template
maps from the "write" commands in APBS and then use a hacked version
of a tool like value.c (or the new multivalue.c!) to modify these maps.
More robust membrane support should be arriving in the future; we're
working on it.
On Dec 22, 2006, at 2:50 AM, Ravinder Abrol wrote:
> Hi All,
> We would like to simulate a protein in an implicit lipid environment,
> which for an accurate description is a multi-dielectric
> environment. Is
> there a way to specify many dielectric (e.g. could be on a grid)
> slabs to
> mimic the lipids?
> Ravinder Abrol
> 139-74, Beckman Institute
> Division of Chemistry and Chemical Engineering
> Caltech, Pasadena, CA 91125
> Phone: 1.626.395.8143
> Fax: 1.626.585.0917
> Email: abrol@...
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Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis