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
FabrÃcio Bracht
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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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