[gmx-users] Help with apolar solvent box

[Justin A. Lemkul]

Ragnarok sdf wrote:
> Hello, I would like to know if there is any recommendation onto
> setting up a system with a protein in a apolar solvent box. If there
> is any tutorial or web page with topologies for solvents. I read that
> the decane box that comes with gromacs is not to be used for
> simulations, if that is true, then how should I assemble my system?
> 

There are a few solvent topologies in the User Contributions section of the 
website.  Other than that, you may have to parameterize the solvent yourself (no 
easy task):

http://wiki.gromacs.org/index.php/Parameterization

-Justin

> Thank you
> Fabrício Bracht
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-- 
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Justin A. Lemkul
Graduate Research Assistant
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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