[gmx-users] GROMACS parameterization

Justin A. Lemkul jalemkul at vt.edu
Sat Aug 1 02:40:31 CEST 2009

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


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