Justin,<br><br><div class="gmail_quote">2011/10/19 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
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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.</blockquote>
<div><br>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 :)<br> </div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br>
You'll never get a good comparison.<br></div></blockquote><div><br>I've tried to analysy my system via your GridMAt software as well as by the GROMACSs functions.<br><br>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.<br>
<br>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?<br>
<br><br><br>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?<br>
<br><br>James<br></div></div>