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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