VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Oct 26 2009 - 10:24:19 CDT

Axel

On Mon, Oct 26, 2009 at 4:08 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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).
>
>
I have performed long simulations of peptides using SPC and SPC/E water
models and in general I observed that it increases the helical content
(compared to experiments). In some cases with peptides that are supposed to
be unstructured in solution, you can observe a large amount of helical
content that does not match the experimental results (even considering that
a peptide does not exist as a fully random coil under highly denaturant
conditions). I personally don't have anything against on in favor when it
comes to particular water models, but I'm just trying to stress on the fact
that it is not recommendable to mix different force fields, either for
technical reasons or because of the physical meaning of the trajectories you
get.

> > 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).
>
>
Even though a convincing proof is always the best option, I'm using my
previous experience with this water model, the CHARMM force field and a bit
of intuition to propose a situation that could likely happen if you combine
both force fields. A larger competition between backbone-backbone and
water-backbone hydrogen bonds might be compensated by the CMAP correction
(if used, of course), so it is still possible that at the end your protein
remains too helical.

Cheers,
Michel

> 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.
>
>