Generalized Born calcs

From: Thomas Bishop (bishop_at_latech.edu)
Date: Tue Aug 16 2011 - 14:53:17 CDT

Dear NAMD 2.8b3

I 'm using the generalized born implicit solvent options for some
calculations and need to know more.
Is there a tutorial or howto or a recent publication w/ NAMD using GB
that I can dig into?

The manual is a bit sparse and may contain some errors.
The default GBIS options give a Debye Screening Length of 9.649 when the
ion concentration is 0.1M
The manual says 10A (is this round-off or not?)
For comparison Amber uses a simpler formula than NAMD
(presumably the same for k = 0.316sqrt([salt]) [mol/L] . Her the 10A
value is obvious.

Many of the NAMD defaults appear to match up with Ambers IGB 5 model.
THanks!

I also have some concern about proper specification of dielectric
In GBIS, the protein dielectric (presumably includes nucleic and lipids
or any non-solvent) is typically of order 1 with solvent at 78.5
Apparently the way to get this configuration in NAMD-GB calcs is to set
value of "Dielectric"
and this gets applied to the protein, e.g. as follow:

dielectric 1.0 # interior dielectric
solventdielectric 78.5

Info: DIELECTRIC 1
Info: GBIS SOLVENT DIELECTRIC: 78.5
Info: GBIS PROTEIN DIELECTRIC: 1

Is this the proper way to specify dielectric constants for solvent and
not-solvent in NAMD GBIS?

Thanks in advance for any tips/tricks/pointers.
TOm

-- 
*******************************
    Thomas C. Bishop
     Tel: 318-257-5209
     Fax: 318-257-3823
http://dna.engr.latech.edu
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