On 7/13/12 6:44 AM, J Peterson wrote:
Thanks Justin,
The explanations are very very useful during my course of simulating a
protein with POPC.
I also would like to get explanation on how to simulate a protein which has
only its N-terminal region embedded in the membrane but the rest in solvent.
What is the easy and accurate way to do it?
Position the protein with editconf -center and follow all the other steps in the
same way. The dimensions of the box become quite important in such a case.
There are some general tips on such placement in another of my tutorials:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/03_tricks.html
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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