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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