[gmx-users] Which membrane result is more reliable?

[Justin A. Lemkul]

Kirill Bessonov wrote:
> Hi Justin,
> 
> Sorry I forgot the attachment. Can you see if these files are ok in 
> terms of sequences and more or less accurately represent both DMPC and 
> DMPE?  they were built in Teilman lab I believe
> 
> DMPE: http://sites.google.com/site/kbessonov/dmpe.itp?attredirects=0&d=1 
> <http://sites.google.com/site/kbessonov/dmpe.itp?attredirects=0&d=1>
> 
> DMPC: http://sites.google.com/site/kbessonov/dmpc.itp?attredirects=0&d=1 
> <http://sites.google.com/site/kbessonov/dmpc.itp?attredirects=0&d=1>
> 

Checking your files for validity is your job, preferably before you run a 
simulation.  There is indeed a DMPC topology from Tieleman's site, but there is 
no DMPE.

> (for some reason attachements do not go through mailing server)
> 
> I was trying to understand causes of helix unwinding after 100ns was due to:
> ---->higher packing density 50 vs 67 A^2/lipid  (I've used membrane 
> boxes before protein insertion on top, just to roughly estimate).
> Could the +/- 15 A^2/lipid error cause this effect of instability?
> 

Again, this is the reason for controls.  Does this compression result because of 
the protein-lipid interaction, or because of the heterogeneity within the lipids.

> --->tried to analyze edr files using g_energy and total energy option, 
> thinking to get potential energy of the system and conclude stability:
> 
> 
> DMPC membrane with 62613 atoms (including water and peptide)
> 
> Energy                      Average       RMSD     Fluct.      Drift  
> Tot-Drift
> -------------------------------------------------------------------------------
> Total Energy                -891474 kJ/mol   1132.81    1131.48 
> -0.00114556   -190.135
> 
> T-Protein                   309.844                  25.3307    25.3304 
> -2.37026e-06  -0.393404
> 
> 
> DMPE membrane with 30416 atoms (including also water and peptide)
> 
> 
> Total Energy:
> Statistics over 100000001 steps [ 0.0000 thru 200000.0156 ps ], 1 data sets
> All averages are exact over 100000001 steps
> 
> Energy                      Average                   RMSD     
> Fluct.         Drift              Tot-Drift
> -------------------------------------------------------------------------------
> Total Energy                -477439 kJ/mol    839.231    790.016 
> -0.0049046    -980.92
> T-Protein_DMPC_DMPE         309.657     3.2719    3.27189 -9.55346e-08 
> -0.0191069
> 
> 
> 
> Is it OK to multiply DMPE total energy ( -477439 kJ/mol ) by factor of 2 
> to correct for atom differences between the membranes or it doesn't make 
> sense? I expect DMPE membrane to have slightly higher total energy due 
> to closer packing.....please advise.
> 

This makes no sense.  "Total energy" is the total energy of the system.  Close 
packing does not necessitate higher energy, if the interactions are favorable.

> -->I have used GridMAT, very cool program, but my results for DMPC 
> membrane were averaging around 80 A^2/lipid, I guess during simulation 
> lipids drift so the density drops (area per lipid increases) ...
> 

This could also be a problem with the simulation parameters.  A pure DMPC 
bilayer gives 80 A^2?  It would seem like something is fundamentally wrong with 
the simulation if that is true.

> 
> What else can I do to make sure that my DMPE result is not bogus (maybe 
> increase are per lipid parameter and rerun  the system again?) and what 
> other analysis tools can I run on my two membrane systems to compare them.
> 

Run controls of pure bilayers with the same simulation parameters.

> Also where can I get more detailed information on g_energy, since menu 
> options are abbreviated and are not 100% clear?
> 

Read the manual.  All of the energy terms are detailed there.  If you want 
specific help on a specific type of analysis, post a more focused question.

-Justin

> Thank you
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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