Positional restraints - Dielectric constant

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Mar 02 2011 - 10:56:18 CST

Hello: Two unrelated questions, about which I was unsure after reading
the 2.8 NAMD manual and web inquiry.

(1) I want to fix the position of both an anion inside a transmembrane
protein (inserted into a POPC bilayer, with TIP3 water around) and its
ligand atoms (acidic proton of neutral GLU and positively charged N of
arginine). Can that be done by simply setting 1 for those atoms in
column B of the PDB file? Submitting the filename.fix file as fixed
atoms for the heating stage after minimization, and subsequent
pressure equilibration and production. Or should I use more complex
harmonic restraints, such as distance colvars?

(2) What about the dielectric constant for such an ensemble, spanning
from 1 for the protein (and the lipid ?) and ca 80 for TIP3? Specific,
authoritative tutorial, such as
<http://mccammon.ucsd.edu/~rlaw/ctbp_workshop_rlaw.htm> do not mention
dielectric.

Thanks for advice

francesco pietra

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