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

[Kirill Bessonov]

Hello Justin,

You helped me before, and I am grateful for that. So basically my summer
research had ended up with the following results:

I have included my *.ipt files this message is long.

*My question: 1)why once simulation is giving  me stable aplha-helix and
other is not if membranes are similar and conditions kept constant.

*                     2) Which result to use, most probale. Does lipid
density might of affected the stability?



->200ns  Simulation of the same peptide in the DMPC only box and in
DMPC/DMPE box [1:1 ratio] but results are different and I want to ask why as
this data will go as part of the paper.

*System:* peptide that is placed on TOP of the membrane, interacting with
lipids (no inserted into the membrane, but floating on top) and above there
are water molecules
*
DMPC membrane simulation - STABLE Peptide Helix, no uncoiling:*

-> 248 DMPC molecules
->Box 9.03 x 9.03 x 10.15 as found at the bottom of gro file (I think this
dimensions are nm units?)
-> Threfore I calculated that Area per Lipid is only: 2facesx90.3^2
A^2/248DMPC = 65.75 A^2/lipid which is low

-> When I was using InflatGro(which I modified to be much more friendly and
accepts 2 lipids) to check the lipid density the values were:
_______________________________________________________________________________________________________

Input *.gro file to shrink or expand:dmpc.gro
Enter  membrane re-scaling factor (default=0.95):*1*
Enter Lipid#1 name (e.g. DMPC):DMPC
Enter Lipid#2 name (e.g. DMPE) otherwise ENTER:
For spacial overlap estimation between lipids...
Please enter distance cutoff value between lipids in A(default = 14):14
Output file name(e.g.'inflated.gro'):rm.gro
Gridsize for area per lipid calculations in A(default = 5):5

TOTAL Area per protein: 1.5 nm^2         or 150.00 A^2
*TOTAL Area per lipid:   0.67  nm^2       or  67.26  A^2*  --> why different
from prev. calculation, slightly smaller?

Area per protein, upper half:  0.000 nm^2        or  0.000 A^2
Area per lipid, upper leaflet :  0.632  nm^2     or 63.210 A^2

Area per protein, lower half:   1.50 nm^2        or 150.00  A^2
Area per lipid, lower leaflet :   0.73  nm^2     or  73.43 A^2
_______________________________________________________________________________________________________

Total Energy:

Statistics over 82987501 steps [ 109970.0078 thru 275945.0000 ps ], 1 data
sets
All averages are exact over 82987501 steps

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/DMPC membrane simulation -> Becomes UNSTABLE after 100ns simulation
time *

-> 93 DMPC and 93 DMPE molecules
->Density: 2faces*68.2*68.2 / 186 lipids = 50 A^2/lipid

-> InflateGro results:
_________________________________________________________________________
TOTAL Area per protein: 0 nm^2   or   0.00 A^2
*TOTAL Area per lipid:   0.49  nm^2       or  48.52  A^2* again smaller?

Area per protein, upper half:  0.000 nm^2        or  0.000 A^2
Area per lipid, upper leaflet :  0.485  nm^2     or 48.517 A^2

Area per protein, lower half:   0.00 nm^2        or   0.00  A^2
Area per lipid, lower leaflet :   0.49  nm^2     or  48.52 A^2

Writing Area per lipid...
Done!
_______________________________________________________________________

DMPC: has 46 atoms and DMPE: has 46 atoms

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




I used the same *.mdp file
*I used following dmpe.ipt  and dmpc files * attached that to my 1st
impression are identical
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