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Re: [ESPResSo-users] Any possibility to define ion in PeptideB

From: Tristan Bereau
Subject: Re: [ESPResSo-users] Any possibility to define ion in PeptideB
Date: Wed, 3 Jul 2013 08:49:01 +0200

Hi Pee,

The model has no neutralizing ions because there's no explicit
electrostatics (some of that effect is contained in the hydrophobic
interactions of the amino acids, though. See the model's paper [Bereau
and Deserno, J. Chem. Phys (2009)] for detail). If you want explicit
ions, you'll need explicit electrostatics for the amino acids
(otherwise the ions won't do you much good)--so you'd need to
reparametrize the force field to take that into account. It's
definitely doable, but can be a bit daunting. We had started tinkering
with Debye-Hueckel potentials, and there is an early implementation of
that in the code. See the $charges==on statement in:

At this point we were trying to correct for the hydrophobic
interactions when turning on charges for the charged amino acids
(because the hydrophobic parametrization contains *some* information
about charged interactions). You may want to look into that, though I
must warn you we never validated anything with that force field. Once
you've parametrized and validated a force field with explicit
electrostatics on the amino acids, you could define new beads for the
ions--that part of the parametrization shouldn't be too difficult.

To define new ions, I'd start looking in src/input/secondary.tcl. This
is where the peptide chain gets built (i.e., putting the atoms at the
right place, bonding them together). Obviously, building an ion is
much simpler! As for the force-field parameters, everything is
contained in the files src/chain_*.tcl.

To answer your last question: there are obvious shortcomings in not
describing electrostatics in a peptide force field. There are a number
of scientific problems for which the current implementation is
flat-out inappropriate, so in that sense you'd be able to tackle a new
class of problems with such a force field.

Hope that helps.


On Wed, Jul 3, 2013 at 8:28 AM, pdam bright <address@hidden> wrote:
> Dear all,
> I am simulating a peptide in Espresso using peptodeB. Now I need to define
> neutralizing ions in my system but I found nothing.
> My question is that if defining ions is possible, where should I do it?
> If not, can I define it by myself? As I've understood, no electrostatic
> potential is present in peptideB, So If I can succeed in defining ions, will
> it be significant?
> Thanks in advance for your kind help,
> Pee

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