Re: SPC/E water model

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Thu Jun 28 2007 - 12:06:29 CDT

Anuradha,

Please be warned that the protein force field parameters in CHARMM were
optimized for use with the TIP3P model for water and its variants. It is
not advisable to use SPC/E with proteins if using the CHARMM force field
directly. If you must use SPC/E, you are better of running your
simulations in GROMACS.
        
----------------------------
Himanshu Khandelia, PhD
Research Assistant Professor (Postdoc)
MEMPHYS, Center for Membrane Physics: www.memphys.sdu.dk
University of Southern Denmark (SDU)
Odense M 5230, Denmark

Phone: +4565503510
email: hkhandel_at_memphys.sdu.dk
WWW: www.memphys.sdu.dk/~hkhandel
-----------------------------

On Thu, 28 Jun 2007, Ilya Chorny wrote:

> Looks in the gromacs topolgy files for SPC/E (spce.itp) and edit the Charmm
> TIP3P water model parameters accordingly (i.e. make changes to the top and
> par files to reflect spc/e). Cut and paste the TIP3 topology rename it SPCE
> and edit accodringly. Also make the necessary changes to the prm file. The
> only difference between SPC/E and TIP3p is the bondlengths/angles and the
> charges.
>
> For SPC/E the charge on the OW is -.8476.
> The OH bodlength is 1.0 A
> The angle is 109.47
>
> For TIP3P the charge on the OW is -.8314.
> The OH bondlength is 1.5A.
> The angle is 104.52.
>
> On 6/28/07, Anuradha Mittal <anuradha.mittal_at_gmail.com> wrote:
> >
> > Hi NAMD users,
> >
> > I want to simulate a protein using SPC/E water models. I have done some
> > search but have not been able to find the parameter files.
> > Can anyone give me some insight into where I can get topology and
> > parameter files which include SPC water model?
> >
> > Thank you all in advance.
> >
> > Anu
> >
>
>
>
> --
> Ilya Chorny Ph.D.
>

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