|Subject:||Re: [ESPResSo-users] Any possibility to define ion in PeptideB|
|Date:||Wed, 3 Jul 2013 12:29:51 +0430|
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,
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