Hi Justin,<br><br>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<br><br>DMPE: <a href="http://sites.google.com/site/kbessonov/dmpe.itp?attredirects=0&d=1">http://sites.google.com/site/kbessonov/dmpe.itp?attredirects=0&d=1</a><br>
<br>DMPC: <a href="http://sites.google.com/site/kbessonov/dmpc.itp?attredirects=0&d=1">http://sites.google.com/site/kbessonov/dmpc.itp?attredirects=0&d=1</a><br><br>(for some reason attachements do not go through mailing server)<br>
<br>I was trying to understand causes of helix unwinding after 100ns was due to:<br>---->higher packing density 50 vs 67 A^2/lipid (I've used membrane boxes before protein insertion on top, just to roughly estimate).<br>
Could the +/- 15 A^2/lipid error cause this effect of instability?<br><br>--->tried to analyze edr files using g_energy and total energy option, thinking to get potential energy of the system and conclude stability:<br>
<br><br>DMPC membrane with 62613 atoms (including water and peptide)<br><br>Energy Average RMSD Fluct. Drift Tot-Drift<br>-------------------------------------------------------------------------------<br>
Total Energy -891474 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>DMPE membrane with 30416 atoms (including also water and peptide)<br>
<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>Total Energy -477439 kJ/mol 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>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.<br>
<br>-->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) ...<br><br><br>
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.<br>
<br>Also where can I get more detailed information on g_energy, since menu options are abbreviated and are not 100% clear?<br><br>Thank you <br>