[gmx-users] Modify TIP4P to TIP4P-Ew

[Cai]

Justin, thanks for your reply. I forgot to mention that I would like to use
OPLS-AA force field together with TIP4P-Ew water in my protein-water
simulation. Since TIP4P-Ew is not available in OPLS-AA force field, I still
need to modify TIP4P to TIP4P-Ew. Could you give me some suggestions for
doing this? Do have to touch the source code?



On Sat, Nov 22, 2014 at 5:00 AM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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>    1. Re: Modify TIP4P to TIP4P-Ew (Justin Lemkul)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 21 Nov 2014 16:48:14 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Modify TIP4P to TIP4P-Ew
> Message-ID: <546FB31E.1040808 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/21/14 4:41 PM, Cai wrote:
> > Hi users,
> >
> > The re-parameterized TIP4P-Ew water model shows encouraging agreements
> with
> > experimental results. Since it is now not available in GROMACS, I have to
> > modify the TIP4P water model to TIP4P-Ew according to this paper.
> >
> > (Horn et. al. (2004). Development of an improved four-site water model
> for
> > biomolecular simulations: TIP4P-Ew. *The Journal of Chemical Physics*,
> > *120*(20),
> > 9665?78).
> >
> > Q1:
> > I know how to change the water parameters (angle, rOH, ...) in the
> topology
> > file (***.top/itp) and implement the Ewald-summation (coulombtype = PME).
> > Is that all? It seems the paper also include correction for LJ by
> > multiplying switching function, adding LJ tail, and correction for
> > pressure, which are not easy to do in GROMACS. Any suggestions for doing
> > these?
> >
> > Q2:
> > Is it possible to do that without touching the source code?
> >
>
> The TIP4P-Ew model is already available in all of the Amber force fields
> provided with Gromacs.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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