From: Aron Broom (broomsday_at_gmail.com)
Date: Wed Feb 29 2012 - 08:31:53 CST
1) Implicit solvent simulations do not have periodic boxes, therefore you
do not need to neutralize your system.
2) The effect of ionic strength simply modifies the external dielectric
constant. In an explicit solvent simulation all coulombic forces are
calculated using E=1.0 for the dielectric constant. In implicit solvent
there are two dielectric constants, one through the protein or whatever
other all-atom solute you have, which is still 1.0, and the other through
the implicit solvent which is normally taken to be ~80 for water. Then,
the implicit solvation model attempts to gauge the contribution from each
of these. So if you are calculating the coulombic force inside a protein
from two atoms in the core, the E=1.0. If you are taking an atom on the
surface to some ligand far away it is 80.0, anything else is something
inbetween based on the model which you'd have to read about. Changing the
ionic strength increases the E value for the implicit solvent to something
more than water, such that coulombic forces passing through the implicit
solvent as screened even more than usual.
On Wed, Feb 29, 2012 at 9:04 AM, Prathit Chatterjee <pc20apr_at_yahoo.co.in>wrote:
> Dear NAMD Experts,
> Few days ago I had asked a question regarding ion-concentration and its
> implications of making a system neutral in implicit solevnt if possible
> and/or required. My mail is stated below.
> I would highly appreciate the endeavor if someone enlightens me of this.
> Thanking You
> *From:* Prathit Chatterjee <pc20apr_at_yahoo.co.in>
> *To:* NAMD Mailing list <namd-l_at_ks.uiuc.edu>
> *Sent:* Friday, 24 February 2012 4:49 PM
> *Subject:* namd-l: regarding ion concentration in implicit solvent
> Dear NAMD Experts,
> I want to simulate a peptide in implicit solvent using NAMD_2.8. I needed
> 8 Na+ ( ~0.04 M of Na+) ions to neutralize the overall system while using
> explicit solvent.
> But, in implicit solvent, specifying ion-concentration means adding that
> much of a monovalent salt in the implicit solvated system (as specified in
> the NAMD manual).
> So, is it necessary to neutralize the system even in implicit solvent and
> if so how? Also I need to know the implication of ion-concentration in an
> implicitly solvated system.
> Any kind of advice/ suggestions will be deeply appreciated.
> Thanks in Advance
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:21:42 CST