[gmx-users] Beyond the KALP15 in DPPC tutorial and doing analysis in GROMACS

Thomas Lipscomb linuxborg2 at yahoo.com
Tue Feb 24 00:19:35 CET 2015

Dear gmx-users,
I have finished the KALP15 in DPPC tutorial up to completing the molecular dynamics but not any of the analysis:http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/09_analysis.html

I made one change to the tutorial: using one maximin 3 molecule instead of one KALP15 molecule.
I have bad lipid packing:"The topology says how many atoms the peptide has, but that's totally irrelevant. 
  You have large voids in your system; it's physical nonsense to have lipids 
randomly strewn about the system in between two layers of water, which will just 
diffuse into the vacuum space (if the simulation even runs)."

And the 1 nanosecond simulation time the tutorial recommends is fast but I heard that you need at least 30 nanoseconds to get good data.
So I need help with two things:
One, is there a tutorial or documentation that gives basic information about how to do an analysis because even reading 09_analysis.html I do not know what to do.  The most important part of this is how to I take good pictures because those will go on my poster and in my thesis.
Two, is there anything about the tutorial that I should change to give me better data when I repeat the tutorial, besides extending the simulation time beyond 1 nanosecond?

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