From: Jason Swails (jason.swails_at_gmail.com)
Date: Thu Jul 18 2013 - 18:30:49 CDT
On Thu, Jul 18, 2013 at 2:10 PM, Adrian <adpala_at_hotmail.com> wrote:
> I'm interested in running some simulations using implicit water (as in the
> namd tutorial 1-4, for example), but I notice you are not supposed to
> explicitly ionize your system in such cases, but I do need to consider
> explicitly the ions, as that's my main interest.
> If I add the ions to the the pdb and delete water molecules, would it be
> correct to continue the procedure for GBIS (generalized born implicit
No. Explicit ions will not work with GB implicit solvent (i.e., the
simulations will 'run', but the results will be meaningless). First of
all, implicit solvent simulations are infinitely dilute, so once the ions
diffuse away from the protein they will never come back.
Secondly, ion parameters were not developed for GB. Ion effects are
incorporated into the implicit solvent model via a Debye-like screening
parameter -- see ionConcentration in
http://www.ks.uiuc.edu/Research/namd/2.8/ug/node31.html (Papers on GB will
have more rigorous explanations).
> If not, what would be the correct approach?
If you need to model the structural effects of ions (rather than just their
electrostatic screening effects), then your only solution is to use
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