Re: Positional restraints - Dielectric constant

From: Giacomo Fiorin (
Date: Wed Mar 02 2011 - 13:42:33 CST

Hi Francesco, if you set position restraints on just those two atoms (anion
and hydrogen from the protein), there's a chance that when you go on with a
long MD run, both the membrane and protein drift across the unit cell, but
the Glu hydrogen stays fixed, and this may distort the structure. I think
indeed the safest may well be to set up a distance colvar and a restraint on


---- ----
  Dr. Giacomo Fiorin
  ICMS - Institute for Computational Molecular Science - Temple University
  1900 N 12 th Street, Philadelphia, PA 19122
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On Wed, Mar 2, 2011 at 11:56 AM, Francesco Pietra <>wrote:

> 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
> <> do not mention
> dielectric.
> Thanks for advice
> francesco pietra

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