[gmx-users] GROMACS parameterization
gmx3 at hotmail.com
Mon Aug 3 11:56:31 CEST 2009
Ah, I can make some more advertisement for my own work.
Have a look at this paper:
> Date: Fri, 31 Jul 2009 20:40:31 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] GROMACS parameterization
> rams rams wrote:
> > Hello users,
> > I have a question about the Gromacs parameterization.
> > By using which water model (SPC / SPC/E / TIP3P etc) and their variants,
> > the protein force field parameters in GROMACS were optimized ?
> This information can be found in the primary literature for each force field.
> Further comparative studies can also be found that compare different water
> models with different force fields.
> > Since a few of the properties of proteins depends upon the water models
> > we employ (for instance, SPC water model over estimates the
> > diffusion properties of the proteins by a factor of approx. 2). it is
> > necessary to know which water model needs to be used in the simulation.
> > Thanks in advance.
> > Ram.
> > ------------------------------------------------------------------------
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> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
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