VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Oct 26 2009 - 10:08:08 CDT

On Mon, 2009-10-26 at 15:40 +0100, L. Michel Espinoza-Fonseca wrote:
> Hi Regina,

michel,

> In addition to what Axel said, it is important that you keep in mind
> that SPC water model underestimates the bulk dielectric permitivity by
> about 20%. This means that if you use this water model you will not

please note that regina was asking about SPC/E and there eps0
not so bad, at least according to the very long simulations that
i did about 7 years ago. in the literature you can find a large
variation of results for eps0, since few people have the patience
to run long enough trajectories, or realize that for computing esp0
the system size doesn't matter that much (you can get it from as
little a 64 waters).

> only face the problems that Axel just listed, but also your protein
> will likely become too helical. Things will get even worse if you use
> this water model in combination with the CHARMM force field plus the
> CMAP correction.

not sure, if this argument is convincing without proof from simulations.
the balance between the competing interactions in classical force fields
is very difficult to estimate. specifically for stability of helical
structures, i would like to remark that you also have to consider the
competition for hydrogen bonds, where SPC/E should have a large
energetic advantage over the CHARMM-TIP3P: SPC/E charges are larger
than TIP3P _and_ rOH is longer, so it can get closer (i.e. interact
stronger), specifically as H-bond donor, due to the missing LJ terms
on the hydrogens in SPC/E).

SPC/E was specifically reparametrized from SPC to overcome the
missing self-polarization and thus underestimation of eps0.

cheers,
   axel.

> Best,
> Michel 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.