Distance-dependent dielectrics in NAMD

From: Sarah Harris (sarah.harris_at_ucl.ac.uk)
Date: Mon Nov 10 2003 - 05:05:36 CST


I am hoping to use the Langevin dynamics option in NAMD to run some
implicitly solvated, united atom simulations of aggregating proteins.
The AMBER 84 parameters are specifically designed for a united atom
representation, but require a linear distance dependent dielectric. The
simulations that I wish to run are completely unfeasible in the presence
of explicit water. Unfortunately, it does not appear to be possible to
define distance dependent dielectric functions in NAMD - does anyone
have any ideas? How difficult would it be to alter the source code to
include this?

I am also aware that the H-bonding interactions are defined differently
for the 84 force-field (they are 10-12 rather than 6-12) but I was
hoping to simply refit these parameters to the 6-12 interaction, which
should overcome the problem. However, I cannot see a way around the lack
of a distance dependent dielectric at present, but would very much
appreciate any advice!!!

Many thanks
Sarah Harris

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