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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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