Justin, 2011/10/19 Justin A. Lemkul <jalem...@vt.edu>
> > It won't cause errors, per se, but it does indicate that your system is > not equilibrated (nor should you expect it to be after only 1 ns). After 20 > ns or so of equilibration, most membrane systems should be devoid of > internal water and should be well-equilibrated. It's crear now. At the current stage I've being tried 20ns equilibration of my same system prepared by G_membed so I hope that I'll get better results in this case :) > > You'll never get a good comparison. > I've tried to analysy my system via your GridMAt software as well as by the GROMACSs functions. First of all my system was very stable- the RMSD deviation < 1A and small Rg indicate on the stability of the protein within the membrane as well. Also I've obtain S per lipid by GridMat of 68 A^2 that is good result. Finally, I've analyzed Lateral Diffusion of Lipids- this value vas up to 0.1 nm during 1ns stimulation as well as density for lipids groups ( this was near 200 kg m^-3 for both groups ). What values for two last measurements are normal for such system as KALP in DPPC? Finally I wounder to simulate pure lipid bi layer with different force fields ( e.g I want to test Charmm ff). Could I use the md parametries from the KALP simulation for the pure bi-layer ? What are main differences beetween simulation of the pure bilayer and system with the protein? James
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