From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Oct 26 2009 - 09:40:33 CDT

Hi Regina,

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 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.

Best,
Michel

On Mon, Oct 26, 2009 at 2:48 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Mon, 2009-10-26 at 14:48 +0200, politr_at_huji.ac.il wrote:
>
> hi regina,
>
> > Hi to All,
> > I want to run simulation of peptide by using SPC/E water model .
> > How can I solvate peptide by VMD with SPC/E water? And where can I
> > get
> > topology and parameter files which include SPC/E water? Thanks to all
>
> first of all, i hope that you are aware of the implications, that
> using a different water potential with force field parameters that
> were not parametrized with that water potential in mind, i.e. that
> that you destroy the "balance" between peptide solvation and
> peptide-peptide interaction.
>
> secondly, the best way to proceed is to first generate an equilibrated
> water box with SPC/E water. as you can see from the parameters listed
> at: http://en.wikipedia.org/wiki/Water_model
> SPC/E <http://en.wikipedia.org/wiki/Water_model%0ASPC/E> has a different
> geometry than TIP3P (n.b. the TIP3P in CHARMM
> is not really TIP3P). then create a copy of your parameter file and
> modify the water parameters in it, that would allow you to run the
> simulation.
>
> but as mentioned before, you would have to re-parametrize everything
> else to have a properly balanced force field, so please be _very_
> careful to not overinterpret the results. particularly, using SPC/E
> with CHARMM parameters can be tricky, since SPC/E doesn't have the
> (mostly repulsive) lennard jones term on water hydrogens and even
> large point charges that are further away from the center, so that
> coulomb interactions between SPC/E and peptide atoms will be
> significantly enhanced.
>
> cheers,
> axel.
>
>
> > people who answer to the questions and thank you in advance for answer
> > to this particular question.
> >
> > Regina
> >
> >
> >
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
>