<div class="gmail_quote">Hello Justin,<br><br>You helped me before, and I am grateful for that. So basically my summer research had ended up with the following results:<br><br>I have included my *.ipt files this message is long. <br>
<br><b>My question: 1)why once simulation is giving me stable aplha-helix and other is not if membranes are similar and conditions kept constant.<br>
<br></b> 2) Which result to use, most probale. Does lipid density might of affected the stability?<br><br><br><br>->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.<br>
<br><b>System:</b> 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<br><u><b><br>DMPC membrane simulation - STABLE Peptide Helix, no uncoiling:</b></u><br>
<br>-> 248 DMPC molecules <br>->Box 9.03 x 9.03 x 10.15 as found at the bottom of gro file (I think this dimensions are nm units?)<br>-> Threfore I calculated that Area per Lipid is only: 2facesx90.3^2 A^2/248DMPC = 65.75 A^2/lipid which is low<br>
<br>-> 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:<br>_______________________________________________________________________________________________________<br>
<br>Input *.gro file to shrink or expand:dmpc.gro<br>Enter membrane re-scaling factor (default=0.95):<b>1</b><br>Enter Lipid#1 name (e.g. DMPC):DMPC<br>Enter Lipid#2 name (e.g. DMPE) otherwise ENTER:<br>For spacial overlap estimation between lipids...<br>
Please enter distance cutoff value between lipids in A(default = 14):14<br>Output file name(e.g.'inflated.gro'):rm.gro<br>Gridsize for area per lipid calculations in A(default = 5):5<br><br>TOTAL Area per protein: 1.5 nm^2 or 150.00 A^2<br>
<b>TOTAL Area per lipid: 0.67 nm^2 or 67.26 A^2</b> --> why different from prev. calculation, slightly smaller?<br><br>Area per protein, upper half: 0.000 nm^2 or 0.000 A^2<br>Area per lipid, upper leaflet : 0.632 nm^2 or 63.210 A^2<br>
<br>Area per protein, lower half: 1.50 nm^2 or 150.00 A^2<br>Area per lipid, lower leaflet : 0.73 nm^2 or 73.43 A^2<br>_______________________________________________________________________________________________________<br>
<br>Total Energy:<br><br>Statistics over 82987501 steps [ 109970.0078 thru 275945.0000 ps ], 1 data sets<br>All averages are exact over 82987501 steps<br><br>Energy Average RMSD Fluct. Drift Tot-Drift<br>
-------------------------------------------------------------------------------<br><b>Total Energy -891474 </b>kJ/mol 1132.81 1131.48 -0.00114556 -190.135<br><br>T-Protein 309.844 25.3307 25.3304 -2.37026e-06 -0.393404<br>
<br><br><br><b>DMPE/DMPC membrane simulation -> Becomes UNSTABLE after 100ns simulation time </b><br><br>-> 93 DMPC and 93 DMPE molecules<br>->Density: 2faces*68.2*68.2 / 186 lipids = 50 A^2/lipid<br><br>-> InflateGro results:<br>
_________________________________________________________________________<br>TOTAL Area per protein: 0 nm^2 or 0.00 A^2<br><b>TOTAL Area per lipid: 0.49 nm^2 or 48.52 A^2</b> again smaller?<br><br>Area per protein, upper half: 0.000 nm^2 or 0.000 A^2<br>
Area per lipid, upper leaflet : 0.485 nm^2 or 48.517 A^2<br><br>Area per protein, lower half: 0.00 nm^2 or 0.00 A^2<br>Area per lipid, lower leaflet : 0.49 nm^2 or 48.52 A^2<br><br>Writing Area per lipid...<br>
Done!<br>_______________________________________________________________________<br><br>DMPC: has 46 atoms and DMPE: has 46 atoms<br><br>Total Energy:<br>Statistics over 100000001 steps [ 0.0000 thru 200000.0156 ps ], 1 data sets<br>
All averages are exact over 100000001 steps<br><br>Energy Average RMSD Fluct. Drift Tot-Drift<br>-------------------------------------------------------------------------------<br>
<b>Total Energy -477439 kJ/mol </b> 839.231 790.016 -0.0049046 -980.92<br>T-Protein_DMPC_DMPE 309.657 3.2719 3.27189 -9.55346e-08 -0.0191069<br><br><br><br><br>I used the same *.mdp file<br>
<b>I used following dmpe.ipt and dmpc files </b> attached that to my 1st impression are identical<br><br><br><br></div><br>