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

[Justin Lemkul]

On 2/23/15 6:13 PM, Thomas Lipscomb wrote:
> 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)."
>

Hopefully you've sorted this out; what you built and showed before wasn't even 
really a membrane.

> 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.

Even 30 ns is short for a membrane system.

> 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?

Be sure the force field is good.  Berger parameters are not as good as more 
modern force fields, particularly CHARMM36.  The reason I did the tutorial the 
way I did was because it is instructive in learning not just membrane protein 
systems, but also how GROMACS organizes force fields.

The problem with the question you're asking is a common one - there is no such 
thing as a recipe for analysis of any simulation.  Sure, there are common things 
you'd check and make sure your outcome is sane, but the analysis is part of your 
job as a scientist.  Why are you doing the simulations?  What's the hypothesis? 
  What do you hope to accomplish or demonstrate?  This is the main reason I 
don't delve into much analysis in my tutorials; it makes people think there are 
formulas for "doing analysis."  My attitude is "less button-pushing, more 
science" :)

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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